File ‘extWeibQuant/libs/extWeibQuant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
File ‘factorQR/libs/factorQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘SciViews’ in Rd xrefs
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Familias/libs/Familias.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘far/libs/far.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   3.8Mb
File ‘fAsianOptions/libs/fAsianOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastAdaboost/libs/fastAdaboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.2Mb
Warning: please export TSAN_OPTIONS='ignore_noninstrumented_modules=1' to avoid false positive reports from the OpenMP runtime.!
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  14.9Mb
File ‘FastHCS/libs/FastHCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘ICSNP’, ‘ICS’ in Rd xrefs
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.7Mb
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘fastStat-Ex.R’ failed
The error most likely occurred in:

> ### Name: idi
> ### Title: Perform IDI for logistic and cox regression
> ### Aliases: idi idi.lrm idi.cph idi.coxph
> 
> ### ** Examples
> 
> library(rms)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

> # logistic
> 
> data(lung)
Warning in data(lung) : data set ‘lung’ not found
> 
> lung$status=lung$status-1
> f1=lrm(status~age+sex,lung)
> f2=lrm(status~age+sex+ph.ecog,lung)
> idi(f1,f2)
 _________________________________________
 
     Reclassification table    
 _________________________________________
Error in table(c1, c2, data[, cOutcome]) : 
  all arguments must have the same length
Calls: idi -> idi.lrm -> <Anonymous> -> table
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.4Mb
File ‘fasttime/libs/fasttime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is 69.2Mb
  sub-directories of 1Mb or more:
    libs  68.8Mb
Namespace in Imports field not imported from: ‘fdapace’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘data.table’ ‘ggplot2’ ‘randomcoloR’ ‘sqldf’
  All declared Imports should be used.
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘lattice’ ‘randomForest’ ‘tibble’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘prettycode’
  All declared Imports should be used.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘NlcOptim’ ‘usethis’ ‘xts’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘MLEcens’, ‘Icens’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘attempt’ ‘glue’
  All declared Imports should be used.
Undeclared package ‘FinePop’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ranger’ ‘yardstick’
  All declared Imports should be used.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  38.8Mb
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    lib   12.7Mb
    libs  18.2Mb
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Undeclared package ‘conicfit’ in Rd xrefs
Undeclared packages ‘BinaryEPPM’, ‘extraDistr’, ‘triangle’ in Rd xrefs
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    4.0Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘evaluate’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘paletteer’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Undeclared package ‘mixture’ in Rd xrefs
installed size is 89.6Mb
  sub-directories of 1Mb or more:
    libs  89.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.7Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘Kendall’ in Rd xrefs
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Undeclared packages ‘vcd’, ‘Epi’ in Rd xrefs
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘ForecastCombinations’ in Rd xrefs
Namespace in Imports field not imported from: ‘dtplyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Namespace in Imports field not imported from: ‘decomposedPSF’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘combinat’ ‘genetics’
  Please remove these calls from your code.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘blockCV’ ‘patchwork’ ‘proxy’
  All declared Imports should be used.
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘pkgKitten’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridis’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   6.8Mb
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘fable’ ‘fabletools’ ‘feasts’ ‘ggplot2’ ‘lubridate’ ‘tibble’
  ‘tidyr’ ‘tsibble’ ‘tsibbledata’ ‘urca’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘pcaPP’ ‘snowFT’ ‘wavelets’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   7.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/data/gannet/ripley/R/packages/tests-clang/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Undeclared package ‘DoE.wrapper’ in Rd xrefs
Package suggested but not available for checking: ‘dggrids’
installed size is 68.7Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.6Mb
    help   1.4Mb
    libs  59.9Mb
Error(s) in re-building vignettes:
--- re-building ‘fRLR.Rnw’ using Sweave
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Timing stopped at: 0.073 0.003 0.049

Error: processing vignette 'fRLR.Rnw' failed with diagnostics:
 chunk 4 
Error in frlr2(X, idx1, idx2, Y, COV) : 
  R_Reprotect: only -9 protected items, can't reprotect index -11

--- failed re-building ‘fRLR.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Undeclared packages ‘frm’, ‘frmpd’ in Rd xrefs
Undeclared packages ‘frm’, ‘frmhet’ in Rd xrefs
Undeclared packages ‘frmhet’, ‘frmpd’ in Rd xrefs
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’ ‘neuralnet’ ‘rpart’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata      3.0Mb
    testForder   1.0Mb
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pROC’ ‘reshape2’ ‘survival’
  All declared Imports should be used.
Undeclared package ‘globals’ in Rd xrefs
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Running examples in ‘fwildclusterboot-Ex.R’ failed
The error most likely occurred in:

> ### Name: boottest.felm
> ### Title: Fast wild cluster bootstrap inference for object of class felm
> ### Aliases: boottest.felm
> 
> ### ** Examples
> 
> library(fwildclusterboot)
> library(lfe)
Error in library(lfe) : there is no package called ‘lfe’
Execution halted
Running ‘spelling.R’
  Running ‘tinytest.R’
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("fwildclusterboot")
  + }
  
  test_bootcluster.R............    0 tests    Error in library(lfe) : there is no package called 'lfe'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fwildclusterboot.Rmd’ using rmarkdown
fixest 0.9.0, BREAKING changes! (Permanently remove this message with fixest_startup_msg(FALSE).) 
- In i():
    + the first two arguments have been swapped! Now it's i(factor_var, continuous_var) for interactions. 
    + argument 'drop' has been removed (put everything in 'ref' now).
- In feglm(): 
    + the default family becomes 'gaussian' to be in line with glm(). Hence, for Poisson estimations, please use fepois() instead.
Quitting from lines 41-59 (fwildclusterboot.Rmd) 
Error: processing vignette 'fwildclusterboot.Rmd' failed with diagnostics:
there is no package called 'lfe'
--- failed re-building ‘fwildclusterboot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    bin   9.2Mb
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘webshot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
Undeclared packages ‘gamlss.dist’, ‘gamlss.add’ in Rd xrefs
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Undeclared package ‘gamlss.dist’ in Rd xrefs
Undeclared package ‘hyperSpec’ in Rd xrefs
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   3.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.0Mb
installed size is 73.2Mb
  sub-directories of 1Mb or more:
    libs  72.7Mb
installed size is 74.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     71.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘gausscov/libs/gausscov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘fortunes’, ‘rmsfact’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘functional’ ‘xts’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.0Mb
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    doc      1.0Mb
    libs    31.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘badger’
  All declared Imports should be used.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Undeclared package ‘TreeSim’ in Rd xrefs
Namespace in Imports field not imported from: ‘survAUC’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.5Mb
    libs      1.4Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘pracma’ ‘rlang’
  All declared Imports should be used.
Package required but not available: ‘stringdist’

Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R  10.1Mb
Namespace in Imports field not imported from: ‘repmis’
  All declared Imports should be used.
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.6Mb
Undeclared package ‘bootstrap’ in Rd xrefs
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.0Mb
File ‘genSurv/libs/genSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘phonTools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Undeclared package ‘RiemBase’ in Rd xrefs
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is 82.5Mb
  sub-directories of 1Mb or more:
    libs  81.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   5.9Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘readr’ ‘spatstat’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘geometr.Rmd’ using rmarkdown
Quitting from lines 268-300 (geometr.Rmd) 
Error: processing vignette 'geometr.Rmd' failed with diagnostics:
Problem with `mutate()` column `deciduous`.
ℹ `deciduous = c(T, T, F, F, F, T, T, F, T, T, F)`.
ℹ `deciduous` must be size 0 or 1, not 11.
--- failed re-building ‘geometr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Package suggested but not available for checking: ‘ChAMP’
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’
  All declared Imports should be used.
Note: found 58 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘lubridate’ ‘readr’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pipeR’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘scales’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘XML’
  All declared Imports should be used.
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Undeclared packages ‘glue’, ‘magrittr’ in Rd xrefs
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘do’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘grDevices’ ‘scales’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  17.8Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Undeclared package ‘quantreg’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘gtable’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘productplots’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graph’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘sna’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
Undeclared packages ‘scales’, ‘labeling’ in Rd xrefs
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘glue’ ‘gridExtra’ ‘xts’ ‘zoo’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.1Mb
    testdata   4.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘dplyr’
  ‘ggpmisc’ ‘ggpubr’ ‘ggrepel’ ‘gridExtra’ ‘markdown’ ‘plotly’
  ‘quantreg’ ‘rlang’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘survival’
  ‘survminer’ ‘table1’ ‘tidyr’ ‘zoo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘nomogramFormula’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
Undeclared packages ‘chemometrics’, ‘rlang’ in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Namespace in Imports field not imported from: ‘class’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Undeclared package ‘usethis’ in Rd xrefs
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
Undeclared packages ‘Runuran’, ‘ghyp’ in Rd xrefs
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.1Mb
Undeclared packages ‘ineq’, ‘IC2’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘mockery’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
File ‘GLIDE/libs/GLIDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 65.6Mb
  sub-directories of 1Mb or more:
    libs  64.3Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
installed size is 43.0Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Undeclared package ‘GMMBoost’ in Rd xrefs
installed size is 44.8Mb
  sub-directories of 1Mb or more:
    libs  43.9Mb
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    libs           45.6Mb
    test_data       2.0Mb
    vignette_data   1.1Mb
Namespaces in Imports field not imported from:
  ‘AER’ ‘MASS’ ‘Matrix’ ‘censReg’ ‘effects’ ‘foreign’ ‘lme4’ ‘lmtest’
  ‘nnet’ ‘pBrackets’ ‘plm’ ‘pscl’ ‘sandwich’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘foreach’ in Rd xrefs
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.9Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Undeclared package ‘glmmLasso’ in Rd xrefs
Undeclared package ‘sandwich’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Undeclared package ‘sfsmisc’ in Rd xrefs
Undeclared package ‘repeated’ in Rd xrefs
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rhandsontable’ ‘shiny’ ‘stats’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared package ‘fBasics’ in Rd xrefs
Undeclared packages ‘devtools’, ‘pkgdown’ in Rd xrefs
Undeclared package ‘jsonlite’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘future’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R   6.2Mb
Undeclared package ‘DiceOptim’ in Rd xrefs
installed size is 120.4Mb
  sub-directories of 1Mb or more:
    libs  119.5Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.9Mb
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.5Mb
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘RColorBrewer’ ‘agricolae’ ‘datasets’ ‘devtools’ ‘dplyr’
  ‘ggplot2’ ‘ggpubr’ ‘grid’ ‘gridGraphics’ ‘knitr’ ‘magrittr’ ‘pastecs’
  ‘rmarkdown’ ‘shinyWidgets’ ‘shinycssloaders’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘knitr’ ‘rmarkdown’ ‘spatstat.core’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   3.2Mb
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘quadmesh’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Found the following significant warnings:
  core_minimise_epl.cpp:14:8: warning: 'random_shuffle<double *, int (&)(int)>' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/GreedyEPL.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘rjags’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Undeclared packages ‘repeated’, ‘gnlm’ in Rd xrefs
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Undeclared package ‘nflfastR’ in Rd xrefs
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gte/libs/gte.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   3.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    help   4.5Mb
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘permute’ in Rd xrefs
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘attempt’ ‘corpcor’ ‘glue’ ‘htmltools’ ‘pkgload’ ‘processx’
  ‘tools’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘fields’ ‘lars’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 169.0Mb
  sub-directories of 1Mb or more:
    R       1.3Mb
    java  166.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    HaDeX   4.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gsubfn’ ‘stringr’
  All declared Imports should be used.
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘parsnip’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   1.6Mb
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdlm/libs/hdlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘ggjoy’ ‘isotone’ ‘mvtnorm’ ‘questionr’ ‘rprojroot’
  ‘tidyverse’
  All declared Imports should be used.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.8Mb
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘healthyR’ ‘healthyR.data’ ‘healthyR.ts’
  All declared Imports should be used.
Undeclared packages ‘Sleuth2’, ‘rrcov’, ‘carData’, ‘qqtest’ in Rd xrefs
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  21.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiagrammeRsvg’ ‘Matrix’ ‘bookdown’ ‘captioner’ ‘rsvg’
  All declared Imports should be used.
Undeclared packages ‘sp’, ‘rgeos’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespace in Imports field not imported from: ‘spatstat.linnet’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
':::' call which should be '::': ‘ggplot2:::guide_axis’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hierband/libs/hierband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘nnet’ ‘stats’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘cubature’ ‘mvtnorm’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.5Mb
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hint/libs/hint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HI/libs/HI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘Guerry’, ‘alr4’, ‘agridat’, ‘coin’ in Rd xrefs
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.7Mb
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘here’ ‘readxlsb’ ‘usethis’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
Undeclared packages ‘nlreg’, ‘cond’, ‘marg’ in Rd xrefs
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘dplyr’ ‘ggforce’ ‘ggplot2’ ‘lifecycle’ ‘purrr’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 65.7Mb
  sub-directories of 1Mb or more:
    libs  65.2Mb
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    doc    1.5Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    doc    1.2Mb
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shiny’ ‘wordcloud2’
  All declared Imports should be used.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
Package suggested but not available for checking: ‘flowCore’
Undeclared packages ‘reshape2’, ‘plyr’, ‘caTools’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibdreg/libs/ibdreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘simpleboot’ in Rd xrefs
File ‘Iboot/libs/Iboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
File ‘ICE/libs/ICE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘icesAdvice’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tidyr’
  All declared Imports should be used.
Undeclared packages ‘bayesm’, ‘ChoiceModelR’, ‘RSGHB’ in Rd xrefs
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  27.1Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Undeclared packages ‘sfsmisc’, ‘RColorBrewer’, ‘hexbin’ in Rd xrefs
Namespace in Imports field not imported from: ‘kableExtra’
  All declared Imports should be used.
Undeclared package ‘moments’ in Rd xrefs
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘testit’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘rlecuyer’
  All declared Imports should be used.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘knitr’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.1Mb
Namespaces in Imports field not imported from:
  ‘covr’ ‘magrittr’ ‘roxygen2’
  All declared Imports should be used.
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    dlib-19.20   9.3Mb
    libs         3.8Mb
Undeclared packages ‘bmp’, ‘jpeg’, ‘png’, ‘tiff’ in Rd xrefs
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.1Mb
    include   3.0Mb
    libs     36.6Mb
Found the following significant warnings:
  gies.cpp:793:13: warning: enumeration value 'SD_NONE' not handled in switch [-Wswitch]
See ‘/data/gannet/ripley/R/packages/tests-clang/IMaGES.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘keras’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘haven’
  All declared Imports should be used.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘optimr’
  All declared Imports should be used.
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘raster’ ‘sp’
  All declared Imports should be used.
Undeclared package ‘R.methodsS3’ in Rd xrefs
Namespace in Imports field not imported from: ‘ca’
  All declared Imports should be used.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Undeclared packages ‘quantreg’, ‘effects’, ‘Hmisc’, ‘rockchalk’, ‘pequod’ in Rd xrefs
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘colorspace’ in Rd xrefs
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Undeclared packages ‘RcppEigen’, ‘tripack’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘curl’ ‘readxl’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc   9.6Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Undeclared package ‘nlstools’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘kableExtra’ ‘markdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GlobalOptions’ ‘testthat’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘seqinr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘glmnet’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.7Mb
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘Unicode’ in Rd xrefs
Undeclared package ‘multtest’ in Rd xrefs
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Undeclared package ‘surveillance’ in Rd xrefs
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
Namespace in Imports field not imported from: ‘chemometrics’
  All declared Imports should be used.
Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          16.5Mb
Namespaces in Imports field not imported from:
  ‘fBasics’ ‘reshape’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘GA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ids’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘boot’ ‘fds’ ‘rpart’
  All declared Imports should be used.
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘survC1’
  All declared Imports should be used.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.8Mb
Undeclared package ‘ggplot2’ in Rd xrefs
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kaps/libs/kaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespaces in Imports field not imported from:
  ‘EQL’ ‘univariateML’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.0Mb
Undeclared packages ‘nor1mix’, ‘ks’, ‘sm’, ‘locfit’, ‘orthopolynom’ in Rd xrefs
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
File ‘KFKSDS/libs/KFKSDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Biostrings’ ‘Rsamtools’ ‘rtracklayer’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘fitdistrplus’
  All declared Imports should be used.
File ‘kissmig/libs/kissmig.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘clustMixType’, ‘randomForest’, ‘ClustVarLV’ in Rd xrefs
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘psycho’ ‘rhandsontable’
  ‘shiny’
  All declared Imports should be used.
Undeclared package ‘splancs’ in Rd xrefs
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘mice’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gmp’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  15.0Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘carData’, ‘factoextra’, ‘labstatR’ in Rd xrefs
Undeclared package ‘sampling’ in Rd xrefs
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘GPArotation’ ‘mice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘LANDD/libs/LANDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs             2.2Mb
    shiny-landsepi   1.3Mb
Namespaces in Imports field not imported from:
  ‘callr’ ‘desc’ ‘parallel’ ‘repr’
  All declared Imports should be used.
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LassoNet/libs/LassoNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘VGAM’, ‘tseries’ in Rd xrefs
File ‘lbfgs/libs/lbfgs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbiassurv/libs/lbiassurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘gridExtra’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘data.table’ ‘utf8’
  All declared Imports should be used.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘SnowballC’ ‘beepr’ ‘broom’ ‘chinese.misc’ ‘dplyr’ ‘highcharter’
  ‘htmlwidgets’ ‘ldatuning’ ‘parallel’ ‘plotly’ ‘purrr’ ‘quanteda’
  ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’ ‘shinycssloaders’ ‘shinyjs’
  ‘stringr’ ‘textmineR’ ‘tidyr’ ‘tidytext’ ‘topicmodels’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘reticulate’ ‘tensorflow’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.1Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘statmod’
  All declared Imports should be used.
Undeclared packages ‘purrr’, ‘dplyr’ in Rd xrefs
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/lfe.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   9.7Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  69.8Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Undeclared package ‘LiblineaR’ in Rd xrefs
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      8.5Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
    libs   1.1Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘purrr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘M3C’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ddpcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘data.table’ ‘e1071’ ‘fastmatch’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘knitr’ ‘pROC’ ‘utils’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs      19.7Mb
    testdata   1.3Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lmeNB/libs/lmeNB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘sfsmisc’, ‘mnormt’ in Rd xrefs
installed size is 55.4Mb
  sub-directories of 1Mb or more:
    libs  54.4Mb
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnls’ ‘utils’
  All declared Imports should be used.
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
File ‘locits/libs/locits.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
Undeclared packages ‘logcondens’, ‘colorspace’ in Rd xrefs
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LogitNet/libs/LogitNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘loglognorm/libs/loglognorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Error(s) in re-building vignettes:
Warning: elapsed-time limit of 30 minutes reached for sub-process
--- re-building ‘lolog-ergm.Rmd’ using rmarkdown

Execution halted
--- re-building ‘lolog-introduction.Rmd’ using rmarkdown
--- finished re-building ‘lolog-introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘lolog-ergm.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 47.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  45.6Mb
Namespace in Imports field not imported from: ‘lavaan’
  All declared Imports should be used.
Undeclared packages ‘etable’, ‘xtable’, ‘tables’ in Rd xrefs
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Icens’ ‘interval’
  All declared Imports should be used.
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘robustbase’
  Please remove these calls from your code.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘rpostgis’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.5Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   1.2Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘fs’ ‘progress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘rlang’ ‘torch’
  All declared Imports should be used.
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.9Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   6.6Mb
Package suggested but not available for checking: ‘dittoSeq’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘googlesheets4’ ‘lifecycle’ ‘withr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘testthat’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   1.1Mb
    libs      2.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘reshape’
  All declared Imports should be used.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.3Mb
    libs         28.3Mb
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.4Mb
    libs   4.5Mb
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      10.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘kableExtra’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   9.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.8Mb
File ‘matie/libs/matie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MAT/libs/MAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  10.0Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Undeclared packages ‘dplyr’, ‘plyr’, ‘reshape2’, ‘reshape’ in Rd xrefs
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘logistf’, ‘brglm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘formatR’ ‘utf8’
  All declared Imports should be used.
Undeclared packages ‘RProbSup’, ‘orddom’ in Rd xrefs
Unknown package ‘orddom’ in Rd xrefs
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  11.1Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.5Mb
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Undeclared packages ‘MCMCpack’, ‘bayesm’, ‘msm’ in Rd xrefs
File ‘MCMChybridGP/libs/MCMChybridGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.6Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.2Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  27.9Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘patchwork’ ‘tidyverse’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
Undeclared packages ‘reshape’, ‘simba’, ‘labdsv’, ‘Hmisc’, ‘untb’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  19.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   6.2Mb
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
installed size is 112.0Mb
  sub-directories of 1Mb or more:
    libs  111.3Mb
Namespaces in Imports field not imported from:
  ‘BiocStyle’ ‘Rgraphviz’ ‘fastAdaboost’ ‘graph’ ‘kernlab’ ‘klaR’
  ‘knitr’ ‘randomForest’ ‘reshape2’ ‘rpart’ ‘tools’
  All declared Imports should be used.
Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespace in Imports field not imported from: ‘pacman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Namespace in Imports field not imported from: ‘lmerTest’
  All declared Imports should be used.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘metasens’, ‘robumeta’ in Rd xrefs
installed size is 110.5Mb
  sub-directories of 1Mb or more:
    libs  110.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.2Mb
File ‘MEtest/libs/MEtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘R2WinBUGS’ in Rd xrefs
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs  20.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Undeclared packages ‘hoa’, ‘evir’ in Rd xrefs
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.0Mb
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘Safe-Censoring.Rmd’ using rmarkdown
--- finished re-building ‘Safe-Censoring.Rmd’

--- re-building ‘Safe-Substitution.Rmd’ using rmarkdown
Quitting from lines 93-94 (Safe-Substitution.Rmd) 
Error: processing vignette 'Safe-Substitution.Rmd' failed with diagnostics:
there is no package called 'qdap'
--- failed re-building ‘Safe-Substitution.Rmd’

SUMMARY: processing the following file failed:
  ‘Safe-Substitution.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.8Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Undeclared packages ‘micEconAids’, ‘micEconSNQP’ in Rd xrefs
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GenomicAlignments’ ‘R.utils’ ‘data.table’ ‘magrittr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘config’ ‘desc’ ‘dplyr’ ‘glue’ ‘withr’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    lib    8.6Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘AzureAuth’ ‘R6’ ‘curl’ ‘jsonlite’ ‘vctrs’
  All declared Imports should be used.
Undeclared package ‘riskRegression’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘gmp’ ‘jpeg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
installed size is 119.0Mb
  sub-directories of 1Mb or more:
    libs  118.4Mb
Namespaces in Imports field not imported from:
  ‘pracma’ ‘rstantools’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.4Mb
Undeclared package ‘scatterplot3d’ in Rd xrefs
Undeclared packages ‘pspline’, ‘lme4’ in Rd xrefs
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Undeclared package ‘quantmod’ in Rd xrefs
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘rms’, ‘Hmisc’, ‘genefilter’ in Rd xrefs
Undeclared packages ‘genefilter’, ‘MKmisc’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 316.1Mb
  sub-directories of 1Mb or more:
    libs  315.6Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Undeclared packages ‘lme4’, ‘rstanarm’, ‘dplyr’ in Rd xrefs
Namespace in Imports field not imported from: ‘parsnip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared package ‘roxygen2’ in Rd xrefs
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.7Mb
Undeclared package ‘seewave’ in Rd xrefs
Namespace in Imports field not imported from: ‘here’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ztable’
  All declared Imports should be used.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   8.2Mb
File ‘morse/libs/morse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggformula’ ‘magrittr’ ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggridges’ ‘ggstance’
  All declared Imports should be used.
Undeclared package ‘cubature’ in Rd xrefs
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
Undeclared package ‘graphlayouts’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
Package suggested but not available for checking: ‘CGHcall’
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 76.0Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.8Mb
File ‘mrfse/libs/mrfse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘speedglm’ in Rd xrefs
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.0Mb
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.0Mb
    libs   3.6Mb
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  15.1Mb
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shape’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polycor’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    libs  57.0Mb
installed size is 115.3Mb
  sub-directories of 1Mb or more:
    doc     5.9Mb
    libs  108.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘poweRlaw’ ‘rmutil’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared packages ‘AICcmodavg’, ‘bbmle’, ‘glmulti’, ‘arm’, ‘wgeesel’, ‘ape’, ‘bestglm’, ‘leaps’, ‘glmmTMB’, ‘brglm’, ‘quantreg’, ‘maxlike’, ‘RMark’ in Rd xrefs
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘dosresmeta’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘mvMORPH’ in Rd xrefs
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    22.6Mb
    models   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.7Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
Undeclared packages ‘sSeq’, ‘PoiClaClu’ in Rd xrefs
Package unavailable to check Rd xrefs: ‘sSeq’
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘downloader’ ‘jsonlite’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   6.7Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.6Mb
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘CoDiNA’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error(s) in re-building vignettes:
--- re-building ‘LOS_model.Rmd’ using rmarkdown

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


Attaching package: 'MASS'

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

    select

--- finished re-building ‘LOS_model.Rmd’

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

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

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

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

Loading required package: lattice
--- finished re-building ‘stranded_model.Rmd’

--- re-building ‘synthetic_news_data.Rmd’ using rmarkdown
Quitting from lines 50-57 (synthetic_news_data.Rmd) 
Error: processing vignette 'synthetic_news_data.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
✖ Column `X1` doesn't exist.
--- failed re-building ‘synthetic_news_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
installed size is 30.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.9Mb
    libs          15.5Mb
Undeclared packages ‘cshapes’, ‘mapdata’ in Rd xrefs
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  24.8Mb
Package in Depends field not imported from: ‘proto’
  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:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    examples   5.8Mb
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘s2’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Undeclared packages ‘quadprog’, ‘bvls’ in Rd xrefs
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘bipartite’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘CAMAN’ ‘Hmisc’ ‘latexpdf’ ‘spatstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Undeclared packages ‘logspline’, ‘ks’ in Rd xrefs
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘nser-Ex.R’ failed
The error most likely occurred in:

> ### Name: bhav
> ### Title: Bhavcopy from NSE
> ### Aliases: bhav
> 
> ### ** Examples
> 
> report = bhav("01072021") # Download bhavcopy for 01 July 2021
trying URL 'https://archives.nseindia.com/content/historical/EQUITIES/2021/JUL/cm01JUL2021bhav.csv.zip'
Warning in download.file(bhavurl, temp) :
  cannot open URL 'https://archives.nseindia.com/content/historical/EQUITIES/2021/JUL/cm01JUL2021bhav.csv.zip': HTTP status was '403 Forbidden'
Error in download.file(bhavurl, temp) : 
  cannot open URL 'https://archives.nseindia.com/content/historical/EQUITIES/2021/JUL/cm01JUL2021bhav.csv.zip'
Calls: bhav -> download.file
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bhav.Rmd’ using rmarkdown
trying URL 'https://archives.nseindia.com/content/historical/EQUITIES/2021/JUL/cm01JUL2021bhav.csv.zip'
Quitting from lines 23-27 (bhav.Rmd) 
Error: processing vignette 'bhav.Rmd' failed with diagnostics:
cannot open URL 'https://archives.nseindia.com/content/historical/EQUITIES/2021/JUL/cm01JUL2021bhav.csv.zip'
--- failed re-building ‘bhav.Rmd’

--- re-building ‘bhavpr.Rmd’ using rmarkdown
trying URL 'https://archives.nseindia.com/archives/equities/bhavcopy/pr/PR010721.zip'
Content type 'application/zip' length 330905 bytes (323 KB)
==================================================
downloaded 323 KB

--- finished re-building ‘bhavpr.Rmd’

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

--- re-building ‘fobhav.Rmd’ using rmarkdown
trying URL 'https://archives.nseindia.com/content/historical/DERIVATIVES/2021/JUL/fo01JUL2021bhav.csv.zip'
Quitting from lines 23-26 (fobhav.Rmd) 
Error: processing vignette 'fobhav.Rmd' failed with diagnostics:
cannot open URL 'https://archives.nseindia.com/content/historical/DERIVATIVES/2021/JUL/fo01JUL2021bhav.csv.zip'
--- failed re-building ‘fobhav.Rmd’

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

SUMMARY: processing the following files failed:
  ‘bhav.Rmd’ ‘fobhav.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs  17.5Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Undeclared packages ‘ensurer’, ‘validate’ in Rd xrefs
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   3.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘e1071’ ‘ggthemes’ ‘mlbench’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
installed size is 87.0Mb
  sub-directories of 1Mb or more:
    libs  86.5Mb
Undeclared package ‘lubridate’ in Rd xrefs
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
Namespaces in Imports field not imported from:
  ‘TCGAbiolinks’ ‘gdata’ ‘genefilter’ ‘maftools’ ‘readxl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.7Mb
File ‘onemap/libs/onemap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.4Mb
installed size is 211.5Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    libs    201.2Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
possible bashism in configure line 52 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘formattable’ ‘rintrojs’ ‘shinyBS’ ‘shinyFeedback’ ‘shinyWidgets’
  ‘shinycssloaders’ ‘shinydashboard’ ‘shinydashboardPlus’ ‘shinyjs’
  ‘shinythemes’ ‘splines’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      5.1Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.3Mb
Undeclared packages ‘alabama’, ‘cccp’, ‘nloptr’ in Rd xrefs
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [43s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘ordinalpattern/libs/ordinalpattern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
Undeclared package ‘microplot’ in Rd xrefs
Undeclared package ‘orloca.es’ in Rd xrefs
File ‘ORMDR/libs/ORMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
Undeclared package ‘maxmatching’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   6.0Mb
File ‘osmgeosample/libs/osmgeosample.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
Undeclared package ‘adegenet’ in Rd xrefs
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ozmaps)
  > 
  > test_check("ozmaps")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-maps.R:13:3): we get plot ─────────────────────────────────────
  `ozmap()` produced messages.
  ── Failure (test-maps.R:14:3): we get plot ─────────────────────────────────────
  `ozmap(x = "abs_ced")` produced messages.
  ── Failure (test-maps.R:23:3): we get plot ─────────────────────────────────────
  `ozmap(asp = 20)` produced messages.
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
Undeclared package ‘packClassic’ in Rd xrefs
Undeclared package ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Undeclared package ‘analogue’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘trend’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
File ‘PAMA/libs/PAMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘rstudioapi’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs  49.9Mb
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘geoR’ ‘gstat’ ‘pryr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Undeclared package ‘Familias’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Undeclared packages ‘glmnet’, ‘rstan’, ‘rstanarm’, ‘discrim’, ‘devtools’, ‘broom’ in Rd xrefs
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
Undeclared package ‘pathfindR’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘testthat’ ‘usethis’ ‘utils’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Mfuzz’ ‘SelectBoost’ ‘gplots’ ‘grid’ ‘jetset’ ‘magic’
  ‘msgps’ ‘splines’ ‘stats4’ ‘survival’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    lib  10.0Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Undeclared packages ‘tibble’, ‘data.table’ in Rd xrefs
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.0Mb
Undeclared packages ‘combinat’, ‘unifDAG’ in Rd xrefs
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Undeclared package ‘spatstat.core’ in Rd xrefs
installed size is 134.7Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  131.1Mb
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.1Mb
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘sm’, ‘spdep’ in Rd xrefs
File ‘PDFEstimator/libs/PDFEstimator.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘mlbench’, ‘foreach’, ‘ICEbox’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘Hmisc’, ‘vcd’, ‘VecStatGraphs2D’, ‘mvtsplot’, ‘matrixStats’, ‘RandomFields’, ‘automap’, ‘spsann’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘dvir’ ‘ibdsim2’ ‘paramlink2’ ‘pedbuildr’ ‘segregatr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.2Mb
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘timeSeries’, ‘tseries’, ‘car’, ‘gplots’ in Rd xrefs
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘classInt’, ‘PMCMR’, ‘agricolae’, ‘plotrix’, ‘AICcmodavg’ in Rd xrefs
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.2Mb
    libs   4.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.5Mb
Undeclared package ‘phase1RMD’ in Rd xrefs
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.2Mb
Undeclared package ‘photobiologyLEDs’ in Rd xrefs
installed size is  5.2Mb
  sub-directories of 1Mb or more:
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    help   1.1Mb
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  33.6Mb
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘future’, ‘geiger’, ‘caper’ in Rd xrefs
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘picante’ in Rd xrefs
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
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    libs  11.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
Undeclared packages ‘pkgdown’, ‘htmlwidgets’ in Rd xrefs
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
installed size is 10.9Mb
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plogr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Undeclared package ‘ISOcodes’ in Rd xrefs
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
Undeclared package ‘flexmix’ in Rd xrefs
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
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    data   4.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
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    libs   1.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
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    libs      3.4Mb
Undeclared package ‘BSgenome’ in Rd xrefs
Namespace in Imports field not imported from: ‘regtools’
  All declared Imports should be used.
installed size is 51.3Mb
  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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Undeclared package ‘ecodist’ in Rd xrefs
installed size is  5.7Mb
  sub-directories of 1Mb or more:
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Undeclared packages ‘rags2ridges’, ‘ragt2ridges’ in Rd xrefs
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installed size is 11.0Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Undeclared packages ‘rstan’, ‘R2WinBUGS’, ‘R2jags’, ‘R2OpenBUGS’, ‘nimble’, ‘rjags’, ‘jagsUI’ in Rd xrefs
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  sub-directories of 1Mb or more:
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Undeclared package ‘advclust’ in Rd xrefs
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installed size is 10.0Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  ‘kknn’ ‘neuralnet’ ‘plyr’ ‘randomForest’ ‘rattle’ ‘rpart’ ‘shinyAce’
  ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’ ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘PRIMAL/libs/PRIMAL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘utils’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
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    libs  15.0Mb
Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.
Undeclared packages ‘ipflasso’, ‘mvtnorm’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DT’ ‘rio’ ‘shiny’ ‘shinyjs’ ‘utils’ ‘webp’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
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installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
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    libs      5.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.6Mb
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘optimx’ ‘tidyverse’
  All declared Imports should be used.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Undeclared packages ‘binom’, ‘PropCIs’, ‘BlakerCI’, ‘prevalence’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
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    libs   2.8Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'proDA', 'STRINGdb'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘tidyr’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘qpdf’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.5Mb
Undeclared package ‘entropy’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  38.9Mb
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
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    doc        4.0Mb
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installed size is 49.8Mb
  sub-directories of 1Mb or more:
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installed size is 32.7Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Undeclared packages ‘vctrs’, ‘httr’ in Rd xrefs
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 30 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
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    staticdocs   3.4Mb
installed size is 54.5Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is 86.1Mb
  sub-directories of 1Mb or more:
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installed size is  5.0Mb
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installed size is 12.6Mb
  sub-directories of 1Mb or more:
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installed size is  7.9Mb
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File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
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installed size is 12.7Mb
  sub-directories of 1Mb or more:
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installed size is  7.9Mb
  sub-directories of 1Mb or more:
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Namespaces in Imports field not imported from:
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  All declared Imports should be used.
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installed size is 11.6Mb
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Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
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installed size is 11.1Mb
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installed size is 10.4Mb
  sub-directories of 1Mb or more:
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Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
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Undeclared package ‘PredictABEL’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Running examples in ‘r2dii.analysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: join_ald_scenario
> ### Title: Join a data-loanbook object to the ald and scenario
> ### Aliases: join_ald_scenario
> 
> ### ** Examples
> 
> installed <- requireNamespace("r2dii.data", quietly = TRUE) &&
+   requireNamespace("r2dii.match", quietly = TRUE)
> if (!installed) stop("Please install r2dii.match and r2dii.data")
Error: Please install r2dii.match and r2dii.data
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [30s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(r2dii.analysis)
  > 
  > test_check("r2dii.analysis")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-join_ald_scenario.R:3:1): (code run outside of `test_that()`) ───
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-join_ald_scenario.R:3:0
  ── Error (test-summarize_weighted_production.R:2:1): (code run outside of `test_that()`) ──
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-summarize_weighted_production.R:2:0
  ── Error (test-target_sda.R:2:1): (code run outside of `test_that()`) ──────────
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-target_sda.R:2:0
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
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installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Namespaces in Imports field not imported from:
  ‘asd’ ‘cubature’ ‘data.table’ ‘ggplot2’ ‘multxpert’ ‘survival’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcompadre’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Undeclared packages ‘longitudinal’, ‘gRbase’ in Rd xrefs
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets        9.7Mb
    super-tiny-icons   1.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   7.1Mb
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’ ‘xml2’
  All declared Imports should be used.
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   5.4Mb
Undeclared packages ‘spam’, ‘RandomFields’ in Rd xrefs
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [8s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rankUncertainty)
  > 
  > test_check("rankUncertainty")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-generateIntervals.R:67:3): canonicalize generates distinct endpoints ──
  all(replicate(100, test())) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 369 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs  11.0Mb
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rasterKernelEstimates/libs/rasterKernelEstimates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘crosstalk’ in Rd xrefs
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    libs   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 67.1Mb
  sub-directories of 1Mb or more:
    libs  66.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘deldir’ ‘lifecycle’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘bitops’
  All declared Imports should be used.
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  32.4Mb
Undeclared packages ‘MCMCpack’, ‘gtools’ in Rd xrefs
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘rbiouml.Rnw’ using Sweave
Loading required package: RCurl
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 5 
Error : Gateway Time-out


--- failed re-building ‘rbiouml.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘PZ.bi’ ‘mu_sigma.nc’
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   6.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Undeclared package ‘processx’ in Rd xrefs
Undeclared packages ‘BsMD’, ‘rsm’, ‘AlgDesign’, ‘lhs’ in Rd xrefs
Undeclared packages ‘car’, ‘leaps’, ‘latticeExtra’, ‘rgl’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Undeclared packages ‘e1071’, ‘RcmdrMisc’ in Rd xrefs
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Undeclared package ‘RcppExamples’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    lib    4.8Mb
    libs   1.4Mb
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      39.5Mb
    libs     11.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    lib       2.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      4.0Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs          11.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SingleCellExperiment’ ‘mclust’
  All declared Imports should be used.
Undeclared package ‘Mercator’ in Rd xrefs
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  18.4Mb
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Undeclared packages ‘readMzXmlData’, ‘MALDIquantForeign’ in Rd xrefs
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘MALDIquantForeign’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Undeclared packages ‘tidyselect’, ‘vctrs’ in Rd xrefs
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.5Mb
    doc    2.8Mb
Undeclared package ‘rebus.unicode’ in Rd xrefs
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Undeclared packages ‘workflows’, ‘hardhat’ in Rd xrefs
Package suggested but not available for checking: ‘opencv’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.9Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘SemiPar’ ‘caret’ ‘dplyr’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pkgload’ ‘processx’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
Undeclared package ‘monomvn’ in Rd xrefs
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘rEMM/libs/rEMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘representr.Rmd’ using rmarkdown
Quitting from lines 101-108 (representr.Rmd) 
Error: processing vignette 'representr.Rmd' failed with diagnostics:
there is no package called 'stringdist'
--- failed re-building ‘representr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      3.4Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    examples   1.9Mb
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 53.1Mb
  sub-directories of 1Mb or more:
    libs  51.8Mb
Namespace in Imports field not imported from: ‘iCluster’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Undeclared package ‘Matching’ in Rd xrefs
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.8Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Undeclared packages ‘lpSolve’, ‘ROI’, ‘Rsymphony’ in Rd xrefs
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    fonts     1.5Mb
    libs      2.6Mb
    useNULL   1.9Mb
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   9.6Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.3Mb
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rhmmer)
  > 
  > test_check("rhmmer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-parse.R:11:3): read_tblout works ──────────────────────────────
  `read_tblout(tblout_file)` produced messages.
  ── Failure (test-parse.R:17:3): read_domtblout works ───────────────────────────
  `read_domtblout(domtblout_file)` produced messages.
  ── Failure (test-parse.R:27:3): files with no data do not fail ─────────────────
  `read_domtblout(empty_tblout_file)` produced messages.
  ── Failure (test-parse.R:28:3): files with no data do not fail ─────────────────
  `read_tblout(empty_domtblout_file)` produced messages.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Undeclared packages ‘tseries’, ‘TSA’ in Rd xrefs
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Undeclared packages ‘dtw’, ‘fastcluster’, ‘Rtsne’ in Rd xrefs
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Undeclared package ‘utility’ in Rd xrefs
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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  5.2Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  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 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    extdata  24.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rlist") 
  Loading required package: rlist
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-search.R:30:3): list.search ─────────────────────────────────────
  Error: there is no package called 'stringdist'
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test-search.R:30:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─rlist::list.search(...)
   5.   └─rlist:::tryWithCondition(...)
   6.     └─base::tryCatch(...)
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 282 ]
  Error: Test failures
  Execution halted
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
Found the following files/directories:
  ‘dipper.inp’ ‘mark001.inp’ ‘mark001.out’ ‘mark001.res’ ‘mark001.vcv’
  ‘mark002.inp’ ‘mark002.out’ ‘mark002.res’ ‘mark002.vcv’ ‘mark003.inp’
  ‘mark003.out’ ‘mark003.res’ ‘mark003.vcv’ ‘mark004.inp’ ‘mark004.out’
  ‘mark004.res’ ‘mark004.vcv’ ‘mark005.inp’ ‘mark005.out’ ‘mark005.res’
  ‘mark005.vcv’ ‘mark006.inp’ ‘mark006.out’ ‘mark006.res’ ‘mark006.vcv’
  ‘mark007.inp’ ‘mark007.out’ ‘mark007.res’ ‘mark007.vcv’ ‘mark008.inp’
  ‘mark008.out’ ‘mark008.res’ ‘mark008.vcv’ ‘mark009.inp’ ‘mark009.out’
  ‘mark009.res’ ‘mark009.vcv’ ‘mark010.inp’ ‘mark010.out’ ‘mark010.res’
  ‘mark010.vcv’ ‘mark010V.tmp’ ‘mark010X.tmp’ ‘mark010Y.tmp’
  ‘mark011.inp’ ‘mark011.out’ ‘mark011.res’ ‘mark011.vcv’ ‘mark012.inp’
  ‘mark012.out’ ‘mark012.res’ ‘mark012.vcv’ ‘mark013.inp’ ‘mark013.out’
  ‘mark013.res’ ‘mark013.vcv’
installed size is 66.6Mb
  sub-directories of 1Mb or more:
    libs  65.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   6.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs       1.2Mb
    minizinc   3.3Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 55.1Mb
  sub-directories of 1Mb or more:
    libs  54.5Mb
Undeclared package ‘fortunes’ in Rd xrefs
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
File ‘RMVL/libs/RMVL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Undeclared packages ‘fossil’, ‘raster’ in Rd xrefs
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 89.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     87.5Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 138-144 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
Package suggested but not available for checking: ‘affydata’
Undeclared package ‘distrEx’ in Rd xrefs
Undeclared package ‘ROptEst’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘bridgesampling’ ‘callr’ ‘extraDistr’ ‘psych’ ‘runjags’
  All declared Imports should be used.
Undeclared package ‘svdvisual’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
Undeclared packages ‘mvtnorm’, ‘scatterplot3d’, ‘HH’ in Rd xrefs
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘readroper’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘diptest’ ‘methods’ ‘viridis’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.5Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   5.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
Undeclared package ‘scalreg’ in Rd xrefs
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSclient/libs/RSclient.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘keras’, ‘tensorflow’, ‘devtools’ in Rd xrefs
Namespace in Imports field not imported from: ‘labelled’
  All declared Imports should be used.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  Rserv.c:2150:17: warning: 'RSA_generate_key' is deprecated [-Wdeprecated-declarations]
  oc.c:47:33: warning: 'RAND_pseudo_bytes' is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. 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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  14.4Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  42.8Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘knitr’
  All declared Imports should be used.
installed size is 201.4Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  194.7Mb
Undeclared packages ‘gamm4’, ‘shiny’, ‘biglm’ in Rd xrefs
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
installed size is 199.2Mb
  sub-directories of 1Mb or more:
    lib    34.5Mb
    libs  161.9Mb
Undeclared packages ‘coda’, ‘rstanarm’ in Rd xrefs
installed size is 96.9Mb
  sub-directories of 1Mb or more:
    libs  95.5Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
Undeclared packages ‘gridExtra’, ‘rstanarm’ in Rd xrefs
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Undeclared package ‘flexsurv’ in Rd xrefs
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘lpSolve’, ‘Rglpk’ in Rd xrefs
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R           1.2Mb
    bootstrap   1.6Mb
    data        2.2Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
File ‘RTextTools/libs/RTextTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    rmarkdown   5.1Mb
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.1Mb
    projects   2.8Mb
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  17.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.3Mb
Running examples in ‘rules-Ex.R’ failed
The error most likely occurred in:

> ### Name: rule_fit
> ### Title: General Interface for RuleFit Models
> ### Aliases: rule_fit update.rule_fit
> 
> ### ** Examples
> 
> rule_fit()
RuleFit Model Specification (unknown)

Computational engine: xrf 

> # Parameters can be represented by a placeholder:
> rule_fit(trees = 7)
RuleFit Model Specification (unknown)

Main Arguments:
  trees = 7

Computational engine: xrf 

> 
> # ------------------------------------------------------------------------------
> 
> set.seed(6907)
> rule_fit_rules <-
+   rule_fit(trees = 3, penalty = 0.1) %>%
+   set_mode("classification") %>%
+   fit(Species ~ ., data = iris)
Error: This engine requires some package installs: 'xrf'
Backtrace:
    █
 1. ├─`%>%`(...)
 2. ├─generics::fit(., Species ~ ., data = iris)
 3. └─parsnip::fit.model_spec(., Species ~ ., data = iris)
 4.   └─parsnip:::check_installs(object)
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Cubist-and-RuleFit.Rmd’ using rmarkdown
Quitting from lines 189-197 (Cubist-and-RuleFit.Rmd) 
Error: processing vignette 'Cubist-and-RuleFit.Rmd' failed with diagnostics:
This engine requires some package installs: 'xrf'
--- failed re-building ‘Cubist-and-RuleFit.Rmd’

SUMMARY: processing the following file failed:
  ‘Cubist-and-RuleFit.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rmarkdown’ ‘table1’
  All declared Imports should be used.
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    libs  49.3Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs     49.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
    test   4.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    libs  52.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs    7.4Mb
    yacas   1.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    7.9Mb
    yacas   1.6Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs     31.2Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Undeclared packages ‘magrittr’, ‘rlang’ in Rd xrefs
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs  14.2Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  22.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.3Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    bin  42.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.2Mb
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAVE/libs/SAVE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   4.1Mb
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'pogs'
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
Undeclared packages ‘Iso’, ‘scam’, ‘gam’ in Rd xrefs
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.7Mb
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GiRaF’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Undeclared package ‘randomNames’ in Rd xrefs
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  16.0Mb
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rsbml’
Undeclared packages ‘EDNE.EQ’, ‘T2EQ’ in Rd xrefs
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta predict runif splinefun uniroot
Consider adding
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
Undeclared package ‘SemNetCleaner’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Undeclared packages ‘NetworkToolbox’, ‘SemNetCleaner’ in Rd xrefs
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   2.8Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs    15.7Mb
    models   1.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘airway’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  13.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
Imports includes 41 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   7.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    doc      2.3Mb
    libs     9.0Mb
    sqlite   1.5Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘kableExtra’ ‘tidyverse’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    www  16.5Mb
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘purrr’ ‘shinyBS’ ‘shinydashboard’
  ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    shinyApp  21.4Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    www   9.0Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.1Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'

Imports includes 28 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Packages unavailable to check Rd xrefs: ‘TFBSTools’, ‘motifmatchr’, ‘chromVAR’
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Undeclared packages ‘ade4’, ‘labdsv’, ‘sp’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Undeclared packages ‘GenOrd’, ‘PoisNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘simFrame-eusilc.Rnw’ using Sweave
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel
--- finished re-building ‘simFrame-eusilc.Rnw’

--- re-building ‘simFrame-intro.Rnw’ using Sweave
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel

Error: processing vignette 'simFrame-intro.Rnw' failed with diagnostics:
 chunk 23 
Error in library("robCompositions") : 
  there is no package called ‘robCompositions’

--- failed re-building ‘simFrame-intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.2Mb
Undeclared packages ‘BinNonNor’, ‘PoisNor’, ‘PoisBinOrdNor’, ‘PoisBinOrdNonNor’ in Rd xrefs
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package suggested but not available for checking: ‘clipper’
Error(s) in re-building vignettes:
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Quitting from lines 263-269 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'clipper'
--- failed re-building ‘simPATHy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘jsonlite’ ‘readr’ ‘shinycssloaders’ ‘tibble’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  19.4Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   7.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘Hmisc’ ‘boot’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Undeclared package ‘RcmdrPlugin.SLC’ in Rd xrefs
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Undeclared packages ‘InformationValue’, ‘ggthemes’ in Rd xrefs
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.3Mb
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.7Mb
    libs  11.2Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rgeos’
  All declared Imports should be used.
Undeclared package ‘RcppArmadillo’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiocStyle’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.6Mb
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
Running examples in ‘solitude-Ex.R’ failed
The error most likely occurred in:

> ### Name: isolationForest
> ### Title: Fit an Isolation Forest
> ### Aliases: isolationForest
> 
> ### ** Examples
> 
> data("humus", package = "mvoutlier")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘mvoutlier’
Calls: data -> find.package
Execution halted
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.2Mb
    libs   6.4Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘testthat’ in Rd xrefs
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Package suggested but not available for checking: ‘DropletUtils’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.1Mb
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.3Mb
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘colorSpec’ in Rd xrefs
Undeclared package ‘rebus.base’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Require’
  All declared Imports should be used.
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs  34.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Imports includes 31 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
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    java   3.3Mb
Undeclared packages ‘splancs’, ‘spatstat.data’ in Rd xrefs
Namespaces in Imports field not imported from:
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  All declared Imports should be used.
Undeclared package ‘sparsebn’ in Rd xrefs
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    help   1.7Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘tibble’ ‘viridisLite’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  20.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘ggplot2’ ‘parallel’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
    libs   1.1Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   9.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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   1.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.1Mb
    etc   1.4Mb
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xcms’
  All declared Imports should be used.
Packages suggested but not available for checking: 'qdap', 'rcytoscapejs'

Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘specmine.datasets’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Undeclared packages ‘reshape2’, ‘sampling’, ‘dplyr’ in Rd xrefs
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      2.9Mb
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggridges’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘RColorBrewer’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘car’ ‘knitr’ ‘lmtest’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  47.6Mb
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Undeclared packages ‘RColorBrewer’, ‘colorspace’ in Rd xrefs
Namespace in Imports field not imported from: ‘sessioninfo’
  All declared Imports should be used.
installed size is 76.6Mb
  sub-directories of 1Mb or more:
    libs  76.2Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Undeclared packages ‘pryr’, ‘functional’, ‘dplyr’, ‘ks’, ‘purrr’, ‘data.table’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘workflowsets’ ‘yardstick’
  All declared Imports should be used.
Undeclared packages ‘h2o’, ‘SuperLearner’ in Rd xrefs
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    include  10.7Mb
    lib       3.0Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    4.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
Undeclared package ‘HDoutliers’ in Rd xrefs
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   9.7Mb
Namespace in Imports field not imported from: ‘dbscan’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/stringdist.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘utf8’
  All declared Imports should be used.
File ‘SummaryLasso/libs/SummaryLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc  10.9Mb
Namespaces in Imports field not imported from:
  ‘psych’ ‘referenceIntervals’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘backports’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Undeclared package ‘truncdist’ in Rd xrefs
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.6Mb
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 138.1Mb
  sub-directories of 1Mb or more:
    libs  137.2Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘readr’ ‘rlang’ ‘survival’ ‘tidyverse’ ‘utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Undeclared package ‘survJamda’ in Rd xrefs
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  12.6Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   7.1Mb
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘svyPVpack-Ex.R’ failed
The error most likely occurred in:

> ### Name: svyPVquantile
> ### Title: Quantile estimation
> ### Aliases: svyPVquantile
> ### Keywords: quantile
> 
> ### ** Examples
> 
> data(svy_example1)
> 
> erg_q <- svyPVquantile(by = ~ sex, svydat=svy.exrep,
+ pvs=c("plaus1","plaus2","plaus3"), quantile=c(0.2,0.7))
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: svyPVquantile -> pv_quantile -> lapply -> FUN -> colnames<-
Execution halted
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mapdata’ ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
possible bashism in configure line 12 (echo -n):
  echo -n "  checking for Sun Studio compiler..."
  possible bashism in configure line 22 (echo -n):
  echo -n "  checking for OS..."
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Undeclared package ‘mlbench’ in Rd xrefs
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
Running examples in ‘tab-Ex.R’ failed
The error most likely occurred in:

> ### Name: tabmedians.svy
> ### Title: Create Table Comparing Group Medians (for Complex Survey Data)
> ### Aliases: tabmedians.svy
> 
> ### ** Examples
> 
> # Create survey design object
> library("survey")
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart

> design <- svydesign(
+   data = tabsvydata,
+   ids = ~sdmvpsu,
+   strata = ~sdmvstra,
+   weights = ~wtmec2yr,
+   nest = TRUE
+ )
> 
> # Compare median BMI by sex
> (medtable1 <- tabmedians.svy(BMI ~ Sex, design = design))
Error in abs(medians) : non-numeric argument to mathematical function
Calls: tabmedians.svy
Execution halted
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.0Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘duckdb’ ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jsonlite’ ‘knitr’ ‘lazyeval’ ‘tidyr’
  All declared Imports should be used.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  11.2Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘psych’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  27.8Mb
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘survivalROC’ in Rd xrefs
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    apps   3.2Mb
    libs  10.0Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.6Mb
    telemac   1.0Mb
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    libs  35.9Mb
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Undeclared packages ‘h2o’, ‘eha’, ‘mfx’, ‘betareg’, ‘brglm’, ‘censReg’, ‘ergm’, ‘latentnet’, ‘fGarch’, ‘gee’, ‘geepack’, ‘gmm’, ‘robustbase’, ‘gnm’, ‘pscl’, ‘robust’, ‘sna’, ‘lqmm’, ‘rms’, ‘erer’, ‘mhurdle’, ‘oglmx’, ‘panelAR’, ‘pglm’, ‘relevent’, ‘quantreg’, ‘spatialreg’, ‘sampleSelection’, ‘RSiena’, ‘simex’, ‘tergm’, ‘survey’, ‘systemfit’, ‘metaSEM’ in Rd xrefs
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   4.3Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Undeclared packages ‘tm’, ‘textreadr’ in Rd xrefs
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘purrr’ ‘readr’
  All declared Imports should be used.
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘graphics’ ‘utils’
  All declared Imports should be used.
Undeclared packages ‘fastDummies’, ‘sjmisc’ in Rd xrefs
Undeclared packages ‘tidyfst’, ‘tidyr’, ‘fastDummies’ in Rd xrefs
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘modeldata’ ‘workflowsets’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘janitor’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dtplyr’ ‘googledrive’ ‘googlesheets4’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is 49.7Mb
  sub-directories of 1Mb or more:
    libs     9.6Mb
    tiledb  38.1Mb
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base64enc’
  All declared Imports should be used.
Undeclared package ‘modeltools’ in Rd xrefs
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    examples  13.5Mb
    include    3.0Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Undeclared packages ‘tm.plugin.dc’, ‘readtext’, ‘graph’, ‘tau’, ‘tokenizers’ in Rd xrefs
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘PROJ’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rappdirs’ ‘withr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fs’ ‘stringr’ ‘torch’ ‘torchvision’ ‘zip’
  All declared Imports should be used.
installed size is 113.7Mb
  sub-directories of 1Mb or more:
    R       4.5Mb
    help    1.4Mb
    libs  107.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘V8’ ‘colorspace’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Undeclared packages ‘g.data’, ‘filehash’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘jpeg’ ‘pastecs’ ‘plyr’ ‘raster’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘boot’ ‘chron’ ‘randtoolbox’
  All declared Imports should be used.
installed size is 124.1Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    libs  119.2Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gsrsb’
  All declared Imports should be used.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘countrycode’ ‘haven’ ‘readstata13’ ‘stringr’ ‘tibble’ ‘tidyr’
  All declared Imports should be used.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Undeclared packages ‘fpc’, ‘clValid’, ‘clv’ in Rd xrefs
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘TSSQLite’, ‘TSMySQL’, ‘TSPostgreSQL’ in Rd xrefs
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.5Mb
Undeclared package ‘rugarch’ in Rd xrefs
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.4Mb
Undeclared package ‘tseries’ in Rd xrefs
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
Undeclared packages ‘multcomp’, ‘agricolae’ in Rd xrefs
Undeclared package ‘randomForest’ in Rd xrefs
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.2Mb
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  50.1Mb
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    shinyapp   3.5Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs       19.4Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    libs      2.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   4.1Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  26.5Mb
Namespaces in Imports field not imported from:
  ‘lavaan’ ‘lifecycle’ ‘patchwork’ ‘ragg’ ‘scales’ ‘simstandard’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.7Mb
    extdata   6.4Mb
Namespaces in Imports field not imported from:
  'parallel' 'xml2'
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘rlang’ ‘tidyverse’
  All declared Imports should be used.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared package ‘candisc’ in Rd xrefs
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘coin’, ‘Hmisc’ in Rd xrefs
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
Undeclared packages ‘ade4’, ‘cclust’, ‘bipartite’, ‘labdsv’, ‘ellipse’, ‘vegan3d’, ‘coda’, ‘maptools’, ‘ape’, ‘picante’ in Rd xrefs
Undeclared packages ‘mclust’, ‘e1071’ in Rd xrefs
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.8Mb
Namespaces in Imports field not imported from:
  ‘plotrix’ ‘sp’ ‘viridis’
  All declared Imports should be used.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Undeclared packages ‘foreach’, ‘copula’ in Rd xrefs
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undeclared packages ‘vioplot’, ‘beanplot’, ‘beeswarm’, ‘parviol’ in Rd xrefs
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   6.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
Namespace in Imports field not imported from: ‘parcats’
  All declared Imports should be used.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘colorspace’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Error(s) in re-building vignettes:
--- re-building ‘Vignette.rmd’ using rmarkdown

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

-----------------------
                      
Welcome to volcano3D!
                      
-----------------------
Could not fetch https://www.r-pkg.org/badges/version/volcano3D
HttpExceptionRequest Request {
  host                 = "www.r-pkg.org"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/badges/version/volcano3D"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout
Error: processing vignette 'Vignette.rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘Vignette.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 74.3Mb
  sub-directories of 1Mb or more:
    libs  73.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    libs  74.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘jsonlite’
  ‘leaflet.extras’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘sp’ ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘flextable’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lemon’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

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

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 70-78 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
there is no package called 'fuzzyjoin'
--- failed re-building ‘united_nations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Undeclared package ‘WikipediR’ in Rd xrefs
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Undeclared packages ‘wpp2010’, ‘wpp2012’ in Rd xrefs
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    extdata   2.4Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.1Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/x13binary.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ggdendro’
  All declared Imports should be used.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      1.8Mb
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    libs  41.5Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/bettermc.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blaise)
  > 
  > test_check("blaise")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_types.R:164:3): empty STRING ──────────────────────────────────
  rep(NA_character_, 10) not equal to dfnew[["A"]].
  Lengths differ: 10 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 419 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/cairoDevice.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
Compilation used the following non-portable flag(s):
  ‘-Werror=implicit-function-declaration)’
Found the following files/directories:
  ‘emeScheme’
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/data/gannet/ripley/R/packages/tests-devel/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘fRLR.Rnw’ using Sweave
Warning: stack imbalance in 'withVisible', 33 then 20
Found the following files/directories:
  ‘schlegel’
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘pritikin-schmidt.Rnw’ using knitr

Quitting from lines 1565-1578 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
The job for model 'container2' exited abnormally with the error message: User interrupt
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  gies.cpp:793:12: warning: enumeration value ‘SD_NONE’ not handled in switch [-Wswitch]
See ‘/data/gannet/ripley/R/packages/tests-devel/IMaGES.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘pkgbuild’
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/lfe.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.2/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘international-mortality-tables-overview.Rmd’ using rmarkdown
Quitting from lines 235-237 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
could not find function "whittaker"
--- failed re-building ‘international-mortality-tables-overview.Rmd’

--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Loading required package: ggplot2
--- finished re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following file failed:
  ‘international-mortality-tables-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [53s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1612 ]
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘veryImportantPackage’
Found the following files/directories:
  ‘Minimal-concordance.tex’ ‘Minimal.Rnw’ ‘Minimal.pdf’
  ‘Minimal.synctex.gz’ ‘Minimal.tex’ ‘figure’
Running ‘spelling.R’
  Running ‘testthat.R’ [29s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(r2dii.analysis)
  > 
  > test_check("r2dii.analysis")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-join_ald_scenario.R:3:1): (code run outside of `test_that()`) ───
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-join_ald_scenario.R:3:0
  ── Error (test-summarize_weighted_production.R:2:1): (code run outside of `test_that()`) ──
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-summarize_weighted_production.R:2:0
  ── Error (test-target_sda.R:2:1): (code run outside of `test_that()`) ──────────
  Error: there is no package called 'r2dii.match'
  Backtrace:
      █
   1. └─base::library(r2dii.match) test-target_sda.R:2:0
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/data/gannet/ripley/R/packages/tests-devel/RDieHarder.Rcheck/00install.out’ for details.
Found the following files/directories:
  ‘4.2’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rhmmer)
  > 
  > test_check("rhmmer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-parse.R:11:3): read_tblout works ──────────────────────────────
  `read_tblout(tblout_file)` produced messages.
  ── Failure (test-parse.R:17:3): read_domtblout works ───────────────────────────
  `read_domtblout(domtblout_file)` produced messages.
  ── Failure (test-parse.R:27:3): files with no data do not fail ─────────────────
  `read_domtblout(empty_tblout_file)` produced messages.
  ── Failure (test-parse.R:28:3): files with no data do not fail ─────────────────
  `read_tblout(empty_domtblout_file)` produced messages.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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. 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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'chromVAR', 'TFBSTools', 'motifmatchr'
Found the following files/directories:
  ‘devtools’
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/stringdist.Rcheck/00install.out’ for details.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.1Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/AnthropMMD.Rcheck/00install.out' for details.
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  34.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    extdata   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Running examples in 'arealDB-Ex.R' failed
The error most likely occurred in:

> ### Name: makeExampleDB
> ### Title: Build an example database
> ### Aliases: makeExampleDB
> 
> ### ** Examples
> 
> # to merely register a set of files
> makeExampleDB(until = "regTable")
I have created a new project directory.
  -> please run 'setVariables()' to create a translation table for territories.
please type in the path to the local folder where the licence is stored: 
Error: Cannot open file for writing:
* 'D:\temp\RtmpEtTZDC\newDB\inv_dataseries.csv'
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    libs  15.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/artemis.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.1Mb
    misc   2.1Mb
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/audio.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'BiocInstaller'
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2021-07-21 r80649) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/baggr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BALD.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.1Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bayes4psy.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Package suggested but not available for checking: 'doMC'
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bayesGAM.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/beanz.Rcheck/00install.out' for details.
Running examples in 'beautier-Ex.R' failed
The error most likely occurred in:

> ### Name: check_empty_beautier_folder
> ### Title: Check there are no files in the default beautier folder
> ### Aliases: check_empty_beautier_folder
> 
> ### ** Examples
> 
> check_empty_beautier_folder()
Error in check_empty_beautier_folder() : Files found in beautier folder. 
beautier_folder: C:\Users\CRAN\AppData\Local/beautier/beautier/Cache 
length(list.files(beautier_folder))): 3 
head(list.files(beautier_folder)): C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/file13670ff35c02,C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/file178c45757dd,C:\Users\CRAN\AppData\Local/beautier/beautier/Cache/fileb9f87bd32678
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bellreg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bettermc.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.9Mb
    libs   1.2Mb
installed size is 144.4Mb
  sub-directories of 1Mb or more:
    include  143.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
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:
  '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.
Error(s) in re-building vignettes:
--- re-building 'bkmrhat-vignette.Rmd' using knitr
For guided examples, go to 'https://jenfb.github.io/bkmr/overview.html'
Loading required package: coda
Diagnostics and parallel chain functioning for Bayesian kernel machine regression
Quitting from lines 41-54 (bkmrhat-vignette.Rmd) 
Error: processing vignette 'bkmrhat-vignette.Rmd' failed with diagnostics:
Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: R Under development (unstable) (2021-07-21 r80649); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server 2008 x64 build 6003, Service Pack 2; hostname: CRANWIN)
--- failed re-building 'bkmrhat-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(blaise)
  > 
  > test_check("blaise")
  == Failed tests ================================================================
  -- Failure (test_types.R:164:3): empty STRING ----------------------------------
  rep(NA_character_, 10) not equal to dfnew[["A"]].
  Lengths differ: 10 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 419 ]
  Error: Test failures
  Execution halted
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  URL 'https://www-users.york.ac.uk/~mb55/datasets/darbela.dct': status was 'SSL connect error'
Error in file(con, "r") : 
  cannot open the connection to 'https://www-users.york.ac.uk/~mb55/datasets/darbela.dct'
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/blavaan.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   7.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bmlm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BonEV.Rcheck/00install.out' for details.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
    lib      28.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/bootnet.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/boxr.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/BRugs.Rcheck/00install.out' for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    doc    7.7Mb
    libs   6.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/Cairo.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    pictures   3.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Running examples in 'cbsodataR-Ex.R' failed
The error most likely occurred in:

> ### Name: cbs_get_catalogs
> ### Title: Retrieves the possible catalog values that can be used for
> ###   retrieving data
> ### Aliases: cbs_get_catalogs
> 
> ### ** Examples
> 
> catalogs <- cbs_get_catalogs()
Warning in open.connection(con, "rb") :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': status was 'SSL connect error'
Warning: Failing: http://opendata.cbs.nl/ODataCatalog/Tables?$format=json
Retrying...
Warning in open.connection(con, "rb") :
  URL 'https://opendata.cbs.nl/ODataCatalog/Tables?$format=json': status was 'SSL connect error'
Error in open.connection(con, "rb") : 
  cannot open the connection to 'http://opendata.cbs.nl/ODataCatalog/Tables?$format=json'
Calls: cbs_get_catalogs ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.1Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/cepreader.Rcheck/00install.out' for details.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    include  37.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.7Mb
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion points segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
Running examples in 'compstatr-Ex.R' failed
The error most likely occurred in:

> ### Name: cs_load_year
> ### Title: Create Year List Object
> ### Aliases: cs_load_year
> 
> ### ** Examples
> 
> # create temporary directory
> tmpdir <- tempdir()
> fs::dir_create(paste0(tmpdir,"/data/"))
> 
> # load sample files into temporary directory
> cs_example(path = paste0(tmpdir,"/data/"))
> 
> # prep sample files
> cs_prep_year(path = paste0(tmpdir,"/data/"))
> 
> # load sample files
> yearList17 <- cs_load_year(path = paste0(tmpdir,"/data/"))
> 
> # delete data
> fs::dir_delete(paste0(tmpdir,"/data/"))
Error: [EBUSY] Failed to remove 'D:/temp/RtmpSGa4nz/data/april2017.csv': resource busy or locked
Execution halted
Running examples in 'convey-Ex.R' failed
The error most likely occurred in:

> ### Name: contrastinf
> ### Title: Generalized linearization of a smooth function of survey
> ###   statistics
> ### Aliases: contrastinf
> 
> ### ** Examples
> 
> library(survey)
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

> library(laeken)
> data(eusilc) ; names( eusilc ) <- tolower( names( eusilc ) )
> 
> # linearized design
> des_eusilc <- svydesign( ids = ~rb030 , strata = ~db040 ,  weights = ~rb050 , data = eusilc )
> des_eusilc <- convey_prep(des_eusilc)
> 
> w <- weights(des_eusilc)
> 
> # ratio linearization
> T1 = list(value = sum(w*eusilc$eqincome) , lin = eusilc$eqincome )
> T2 = list(value = sum(w), lin = rep (1, nrow(eusilc)) )
> list_all <- list( T1 = T1, T2 = T2)
> lin_R = contrastinf (quote(T1/T2), list_all)
> 
> # estimate of the variable eqincome mean
> lin_R$value
[1] 19890.81
> # se estimate of the variable eqincome mean
> SE(svytotal(lin_R$lin, des_eusilc))
         [,1]
[1,] 86.82948
> # to check, use
> svymean (~eqincome, des_eusilc)
          mean     SE
eqincome 19891 86.829
> 
> # quintile share ratio (qsr) linearization
> S20 <- svyisq(~ eqincome, design = des_eusilc, .20)
Error in x - incvar : non-numeric argument to binary operator
Calls: svyisq -> svyisq.survey.design -> densfun
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
Package suggested but not available for checking: 'ProData'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Running 'test-all.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > test_check("crminer")
  Loading required package: crminer
  == Skipped tests ===============================================================
  * On CRAN (15)
  
  == Failed tests ================================================================
  -- Error (test-crm_links.R:55:3): crm_links: elife special handling ------------
  Error: res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
  Backtrace:
      x
   1. \-crminer::crm_links("10.7554/elife.04059") test-crm_links.R:55:2
   2.   \-crminer:::crm_works_links(dois = doi, ...)
   3.     +-stats::setNames(lapply(dois, get_links, ...), dois)
   4.     \-base::lapply(dois, get_links, ...)
   5.       \-crminer:::FUN(X[[i]], ...)
   6.         \-crminer:::crm_GET(sprintf("works/%s", x), NULL, FALSE, ...)
   7.           \-base::stopifnot(res$response_headers$`content-type` == "application/json;charset=UTF-8")
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
  Error: Test failures
  Execution halted
Running examples in 'crsra-Ex.R' failed
The error most likely occurred in:

> ### Name: crsra_import_course
> ### Title: Imports all the .csv files into one list consisting of all the
> ###   tables within the course.
> ### Aliases: crsra_import_course
> 
> ### ** Examples
> 
> zip_file = system.file("extdata", "fake_course_7051862327916.zip",
+ package = "crsra")
> bn = basename(zip_file)
> bn = sub("[.]zip$", "", bn)
> res = unzip(zip_file, exdir = tempdir(), overwrite = TRUE)
Error in unzip(zip_file, exdir = tempdir(), overwrite = TRUE) : 
  cannot open file 'D:/temp/RtmpQ9GA5q/fake_course_7051862327916/programming_submission_part_grid_grading_statuses.csv': Invalid argument
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.7Mb
    libs   5.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.6Mb
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.7Mb
    help   1.0Mb
    libs   1.2Mb
Package which this enhances but not available for checking: 'doMC'
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    deps  10.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    lib   8.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    deps   6.5Mb
Error(s) in re-building vignettes:
--- re-building 'datadigest.Rmd' using rmarkdown
pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'datadigest.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'datadigest.Rmd'

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

Error: Vignette re-building failed.
Execution halted
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11343 (sockconn)
Execution halted
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/deeptime.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.8Mb
    help   1.5Mb
    libs   1.1Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   2.8Mb
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11188 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11188 (sockconn)
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    help   1.3Mb
    libs   1.1Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  15.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    assets   2.9Mb
    doc      2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/dowser.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/DSAIDE.Rcheck/00install.out' for details.
Running examples in 'DSSAT-Ex.R' failed
The error most likely occurred in:

> ### Name: add_v_fmt
> ### Title: Adds variable format information to a tibble
> ### Aliases: add_v_fmt
> 
> ### ** Examples
> 
> 
> # Extract file path for sample ecotype file
> sample_eco_file <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
> 
> # Read sample ecotype file
> eco <- read_eco(sample_eco_file)
Error: '@ECO#  ECONAME.........  TBASE  TOPT ROPT   P20  DJTI  GDDE  DSGFT  RUE   KCAN  TSEN  CDAY' does not exist in current working directory ('d:/Rcompile/CRANpkg/local/4.2/DSSAT.Rcheck').
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   2.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
Running 'testthat.R' [65s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  == Failed tests ================================================================
  -- Failure (test-news.R:34:3): update_news works -------------------------------
  `find_news(path = dir_loc)` did not throw an error.
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 554 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    bin       3.2Mb
    extdata   1.7Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Title: Trim and Format Address Information
> ### Aliases: trim_address
> 
> ### ** Examples
> 
> addr_string <- " 2 Dept of Urology, Feinberg School of Medicine," 
> addr_string <- paste(addr_string, "Chicago, US; Dept of Mol Bio as well...")
> print(addr_string)
[1] " 2 Dept of Urology, Feinberg School of Medicine, Chicago, US; Dept of Mol Bio as well..."
> print(trim_address(addr = addr_string))
[1] "Dept of Urology, Feinberg School of Medicine, Chicago, US"
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.82 0.45 488.48 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Error(s) in re-building vignettes:
--- re-building 'FetchingDataFromFRED.Rmd' using rmarkdown
Quitting from lines 51-53 (FetchingDataFromFRED.Rmd) 
Error: processing vignette 'FetchingDataFromFRED.Rmd' failed with diagnostics:
'by' must specify a uniquely valid column
--- failed re-building 'FetchingDataFromFRED.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc       6.1Mb
    extdata   5.1Mb
Running examples in 'EIAdata-Ex.R' failed
The error most likely occurred in:

> ### Name: EIAdata-package
> ### Title: R wrapper for the US Energy Information Administration's (EIA's)
> ###   API.
> ### Aliases: EIAdata-package EIAdata
> ### Keywords: EIAdata
> 
> ### ** Examples
> 
> # The function wngsr will return a list object containing the time
> # the report was run, and the contents of the US EIA's Weekly
> # Natural Gas Storage Report.  The function has no arguments,
> # so simply run:
> 
> wngsr()
Warning in file(file, "rt") :
  URL 'https://ir.eia.gov/ngs/wngsr.csv': status was 'SSL connect error'
Error in file(file, "rt") : 
  cannot open the connection to 'http://ir.eia.gov/ngs/wngsr.csv'
Calls: wngsr -> <Anonymous> -> read.table -> file
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/EpiNow2.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.1Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(evaluator)
  > 
  > # ensure phantom.js is available on CI platforms
  > if (Sys.getenv("NOT_CRAN", "") != "" || Sys.getenv("CI", "") != "") {
  +   if (!shinytest::dependenciesInstalled()) shinytest:::installDependencies()
  +   message("Using phantom.js from ", shinytest:::find_phantom(), "\n")
  + }
  > 
  > test_check("evaluator")
  # Scenario model: openfair_tef_tc_diff_lm
  == Skipped tests ===============================================================
  * Not running MVA test - EVALUATOR_TEST_MVA not set (1)
  * On CRAN (1)
  * Shiny testing is awkward, consider moving to stand along pkg (1)
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test-reports.R:19:1): (code run outside of `test_that()`) ------------
  Error: Cannot open file for writing:
  * 'D:\temp\Rtmpau1qei\inputs\qualitative_scenarios.csv'
  Backtrace:
      x
   1. \-readr::write_csv(...) test-reports.R:19:0
   2.   \-readr::write_delim(...)
   3.     \-vroom::vroom_write(...)
   4.       \-vroom:::vroom_write_(...)
  
  [ FAIL 1 | WARN 1 | SKIP 4 | PASS 136 ]
  Error: Test failures
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.1Mb
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    Rcgi      3.2Mb
    cgi-bin   3.0Mb
Running examples in 'fastStat-Ex.R' failed
The error most likely occurred in:

> ### Name: idi
> ### Title: Perform IDI for logistic and cox regression
> ### Aliases: idi idi.lrm idi.cph idi.coxph
> 
> ### ** Examples
> 
> library(rms)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

> # logistic
> 
> data(lung)
Warning in data(lung) : data set 'lung' not found
> 
> lung$status=lung$status-1
> f1=lrm(status~age+sex,lung)
> f2=lrm(status~age+sex+ph.ecog,lung)
> idi(f1,f2)
 _________________________________________
 
     Reclassification table    
 _________________________________________
Error in table(c1, c2, data[, cOutcome]) : 
  all arguments must have the same length
Calls: idi -> idi.lrm -> <Anonymous> -> table
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/fdrDiscreteNull.Rcheck/00install.out' for details.
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/FGSG.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    lib    3.0Mb
    libs   2.2Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    4.0Mb
    libs   1.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    help   2.2Mb
    libs   3.1Mb
Error(s) in re-building vignettes:
--- re-building 'basic_usage.Rmd' using rmarkdown

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('d:/RCompile/CRANpkg/local/4.2/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building 'basic_usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: 'dggrids'
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.5Mb
    help   1.4Mb
    libs  12.7Mb
Error(s) in re-building vignettes:
--- re-building 'fRLR.Rnw' using Sweave
Warning: stack imbalance in 'withVisible', 33 then 35
Warning: stack imbalance in 'withVisible', 33 then 32

Error: processing vignette 'fRLR.Rnw' failed with diagnostics:
 chunk 4 
Error in structure(new.time - time, class = "proc_time") : 
  R_Reprotect: only 3 protected items, can't reprotect index -2

--- failed re-building 'fRLR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/frscore.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [54s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fusen)
  > 
  > test_check("fusen")
  Writing NAMESPACE
  Writing NAMESPACE
  Writing my_fifth_median.Rd
  Writing my_fourth_median.Rd
  Writing my_median.Rd
  Writing my_other_median.Rd
  Writing sub_median.Rd
  Writing my_third_median.Rd
  Writing NAMESPACE
  Writing NAMESPACE
  Writing my_median.Rd
  Writing NAMESPACE
  Writing NAMESPACE
  Writing my_fourth_median.Rd
  Writing my_median.Rd
  Writing NAMESPACE
  Writing NAMESPACE
  Writing my_median.Rd
  Writing my_other_median.Rd
  Writing sub_median.Rd
  Writing NAMESPACE
  Writing NAMESPACE
  == Failed tests ================================================================
  -- Failure (test-inflate.R:69:5): inflate() output error -----------------------
  grepl("license", check_out[["warnings"]][1]) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 58 ]
  Error: Test failures
  Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    doc   44.4Mb
    libs   1.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.4Mb
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(GBcurves)
  > 
  > test_check("GBcurves")
  == Failed tests ================================================================
  -- Failure (test_gb.R:23:3): Test function -------------------------------------
  nrow(df.out) > 0 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    doc      1.0Mb
    gdal     2.1Mb
    libs    44.8Mb
    proj     8.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   3.2Mb
    libs      1.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R  10.1Mb
Error(s) in re-building vignettes:
--- re-building 'geno2proteoIntroduction.Rnw' using Sweave
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "geno2proteoIntroduction.tex" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'geno2proteoIntroduction.pdf' for vignette with name 'geno2proteoIntroduction' and engine 'utils::Sweave'. The following files exist in working directory 'd:\RCompile\CRANpkg\local\4.2\geno2proteo.Rcheck\vign_test\geno2proteo\vignettes': 'geno2proteoIntroduction.Rnw' (23669 bytes), 'geno2proteoIntroduction.tex' (28094 bytes)
--- failed re-building 'geno2proteoIntroduction.Rnw'

SUMMARY: processing the following file failed:
  'geno2proteoIntroduction.Rnw'

Error: Vignette re-building failed.
Execution halted
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ###   Decimal degrees.
> ### Aliases: sexagesimal
> 
> ### ** Examples
> 
> # Latitude
> g <- -33
> m <- 38
> s <- 30.123456
> value <- sexagesimal(g, m, s, digits = 4)
> print(value)
[1] -33.6417
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  11.46 0.58 12.31 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.6Mb
Error(s) in re-building vignettes:
--- re-building 'geometr.Rmd' using rmarkdown
Quitting from lines 268-300 (geometr.Rmd) 
Error: processing vignette 'geometr.Rmd' failed with diagnostics:
Problem with `mutate()` column `deciduous`.
i `deciduous = c(T, T, F, F, F, T, T, F, T, T, F)`.
i `deciduous` must be size 0 or 1, not 11.
--- failed re-building 'geometr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Running examples in 'ggguitar-Ex.R' failed
The error most likely occurred in:

> ### Name: select_chords
> ### Title: Select chords by criteria
> ### Aliases: select_chords
> 
> ### ** Examples
> 
> select_chords(chord_name = 'Major', string_5_fret = 3)
Warning: `filter_()` was deprecated in dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in if (!is.null(value) && value != "") { : 
  missing value where TRUE/FALSE needed
Calls: select_chords -> narrow_chord
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.1Mb
    testdata   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs           13.7Mb
    test_data       2.0Mb
    vignette_data   1.1Mb
Package suggested but not available for checking: 'cplexAPI'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/graphicalVAR.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'grob_layout.Rmd' using rmarkdown
--- finished re-building 'grob_layout.Rmd'

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

--- re-building 'grobblR.Rmd' using rmarkdown
Quitting from lines 260-278 (grobblR.Rmd) 
Error: processing vignette 'grobblR.Rmd' failed with diagnostics:
The object passed through grob_image() must either be a ggplot object, an existing URL to a .png image or an existing local file path to a .png image.
--- failed re-building 'grobblR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 168.9Mb
  sub-directories of 1Mb or more:
    R       1.2Mb
    java  166.3Mb
Error(s) in re-building vignettes:
--- re-building 'harmonicmeanp.Rmd' using rmarkdown
Quitting from lines 389-402 (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
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hazer)
  > 
  > test_check("hazer")
  == Failed tests ================================================================
  -- Failure (testall.R:22:3): test the haze -------------------------------------
  floor(h$haze * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 225, 224).
  1/1 mismatches
  [1] 224 - 225 == -1
  -- Failure (testall.R:23:3): test the haze -------------------------------------
  floor(h$A0 * 1000) not equal to ifelse(tolower(Sys.info()[[1]]) != "linux", 710, 712).
  1/1 mismatches
  [1] 712 - 710 == 2
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
  Error: Test failures
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Package suggested but not available for checking: 'ie2miscdata'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
> model$output$fit
[1] 0.4515827
> model$output$gradient
x1 
 0 
> model$output$hessian
   x1
x1  8
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.65 0.47 8.19 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   6.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.9Mb
    libs         1.3Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.4Mb
    extdata   1.0Mb
    include   3.0Mb
    libs      7.8Mb
Found the following significant warnings:
  gies.cpp:793:12: warning: enumeration value 'SD_NONE' not handled in switch [-Wswitch]
See 'd:/Rcompile/CRANpkg/local/4.2/IMaGES.Rcheck/00install.out' for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs   10.1Mb
    share  10.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.2Mb
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "polygon",
             "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
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.
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11972 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11972 (sockconn)
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app    4.2Mb
    data   1.5Mb
Packages in Depends field not imported from:
  'MASS' 'VGAM' 'apTreeshape' 'ape' 'geiger' 'gtools' 'partitions'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.2Mb
Error(s) in re-building vignettes:
--- re-building 'janitor.Rmd' using rmarkdown

Attaching package: 'janitor'

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

    chisq.test, fisher.test

pandoc.exe: Unknown extension: gfm_auto_identifiers
Error: processing vignette 'janitor.Rmd' failed with diagnostics:
pandoc document conversion failed with error 7
--- failed re-building 'janitor.Rmd'

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

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

--- finished re-building 'tabyls.Rmd'

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

Error: Vignette re-building failed.
Execution halted
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   4.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/lfe.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'doMC'
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    extdata   1.1Mb
    libs      1.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.0Mb
    libs       1.2Mb
    testdata   1.3Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  d:/RCompile/CRANpkg/lib/4.2/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.2/lolog.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    help   1.2Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   4.0Mb
Found the following significant warnings:
  lxb.c:62:21: warning: '%d' directive writing between 1 and 11 bytes into a region of size 4 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.2/lxb.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs  36.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    libs   1.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs          3.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.4Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs       1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/MDSMap.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs   2.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.2Mb
    lib    1.0Mb
    libs   1.1Mb
cdf.pval: no visible global function definition for 'median'
cdf.pval: no visible binding for global variable 'ecdf'
find_hits: no visible global function definition for 'na.omit'
mad.scores: no visible global function definition for 'as.formula'
mad.scores: no visible binding for global variable 'median'
mad.scores: no visible binding for global variable 'mad'
rm.outliers: no visible global function definition for 'as.formula'
rm.outliers: no visible binding for global variable 'median'
rm.outliers: no visible binding for global variable 'mad'
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/MIRES.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   4.1Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/mpmi.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   4.0Mb
    libs   1.1Mb
Running 'test-all.R' [85s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  == Skipped tests ===============================================================
  * On CRAN (2)
  
  == Failed tests ================================================================
  -- Error (test-mudata-io.R:114:3): type strs are guessed when inappropriate columns exist in columns tbl --
  Error: Error writing mudata to CSV:
   _mudata.csv: Error : Cannot open file for writing:
  * 'D:\temp\RtmpOkxNcg\filec3d8c4f49c2\_mudata.csv'
  
  Backtrace:
      x
   1. \-mudata2::write_mudata_dir(...) test-mudata-io.R:114:2
  
  [ FAIL 1 | WARN 1 | SKIP 2 | PASS 891 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'leukemiasEset'
Error(s) in re-building vignettes:
--- re-building 'Tutorial.Rmd' using rmarkdown


Quitting from lines 131-144 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
Bioconductor does not yet build and check packages for R version 4.2; see
  https://bioconductor.org/install
--- failed re-building 'Tutorial.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    5.8Mb
    libs   5.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs     2.3Mb
    models   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
--- re-building 'LOS_model.Rmd' using rmarkdown

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


Attaching package: 'MASS'

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

    select

--- finished re-building 'LOS_model.Rmd'

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

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

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

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

Loading required package: lattice
--- finished re-building 'stranded_model.Rmd'

--- re-building 'synthetic_news_data.Rmd' using rmarkdown
Quitting from lines 50-57 (synthetic_news_data.Rmd) 
Error: processing vignette 'synthetic_news_data.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
x Column `X1` doesn't exist.
--- failed re-building 'synthetic_news_data.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    CppCode   1.6Mb
    R         5.8Mb
    include   5.8Mb
    libs      1.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.3Mb
    libs   1.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
--- re-building 'ojsr-vignette.Rmd' using rmarkdown
Quitting from lines 260-268 (ojsr-vignette.Rmd) 
Error: processing vignette 'ojsr-vignette.Rmd' failed with diagnostics:
object 'record' not found
--- failed re-building 'ojsr-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
Undefined global functions or variables:
  optim par x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/OpenCL.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'unix'
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs   12.6Mb
    share  10.2Mb
Error(s) in re-building vignettes:
--- re-building 'openland_vignette.Rmd' using rmarkdown
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Quitting from lines 40-52 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
cannot open URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
--- failed re-building 'openland_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     3.9Mb
    models   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
Running 'exporting-methods.R' [4s]
  Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  == Failed tests ================================================================
  -- Error (test.match_on.R:591:5): standardization_scale with svyglm ------------
  Error: non-numeric argument to binary operator
  Backtrace:
      x
   1. \-optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   \-optmatch:::standardizer(des_t)
   3.     +-stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     \-survey:::update.survey.design(...)
   5.       \-base::eval(dots[[j]], object$variables, parent.frame())
   6.         \-base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs   3.0Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/pbdRPC.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    lib    2.8Mb
    libs   2.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   1.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   6.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  12.8Mb
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11942 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11942 (sockconn)
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    application   4.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.1Mb
    libs   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      1.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   1.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      1.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/pryr.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.3Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs      2.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   1.2Mb
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.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   1.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
Error(s) in re-building vignettes:
--- re-building 'rbiouml.Rnw' using Sweave
Loading required package: RCurl
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 5 
Error in queryJSON("/web/table/createTable", params = c(de = path, columns = toJSON(columns),  : 
  Error communicating with SQL server.

--- failed re-building 'rbiouml.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.2/Rblpapi.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/Rcplex.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    libs      1.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       1.9Mb
    libs      1.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.1Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.4Mb
    libs      1.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs           1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/rcrypt.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.5Mb
    doc    2.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Package which this enhances but not available for checking: 'Rcplex'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    doc        3.4Mb
    gdal       2.2Mb
    libs      43.1Mb
    pictures   1.3Mb
    proj       8.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   2.8Mb
    libs      3.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc     1.7Mb
    fonts   1.5Mb
    libs    1.3Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   2.4Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc          10.3Mb
    htmlwidgets   1.2Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rhmmer)
  > 
  > test_check("rhmmer")
  == Failed tests ================================================================
  -- Failure (test-parse.R:11:3): read_tblout works ------------------------------
  `read_tblout(tblout_file)` produced messages.
  -- Failure (test-parse.R:17:3): read_domtblout works ---------------------------
  `read_domtblout(domtblout_file)` produced messages.
  -- Failure (test-parse.R:27:3): files with no data do not fail -----------------
  `read_domtblout(empty_tblout_file)` produced messages.
  -- Failure (test-parse.R:28:3): files with no data do not fail -----------------
  `read_tblout(empty_domtblout_file)` produced messages.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.2/Rhpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.2/RInside.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.2Mb
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_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/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. 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.
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 24.6Mb
  sub-directories of 1Mb or more:
    extdata  23.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    minizinc   2.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      3.1Mb
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
Quitting from lines 138-144 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
--- failed re-building 'intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    1.7Mb
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/ROracle.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/RPostgreSQL.Rcheck/00install.out' for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.2/RSclient.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.2/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.2/Rserve/libs/x64/Rserve.dll':
  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', '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. 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.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.2/RSNNS.Rcheck/00install.out' for details.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3.99 0.12 4.12 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.5Mb
    libs   9.3Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    lib    2.0Mb
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/rstap.Rcheck/00install.out' for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2021-05-18 r80323)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.2.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.1Mb
    projects   2.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   2.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Running examples in 'rvest-Ex.R' failed
The error most likely occurred in:

> ### Name: google_form
> ### Title: Make link to google form given id
> ### Aliases: google_form
> ### Keywords: internal
> 
> ### ** Examples
> 
> google_form("1M9B8DsYNFyDjpwSK6ur_bZf8Rv_04ma3rmaaBiveoUI")
Error in read_html.response(httr::GET(paste0("https://docs.google.com/forms/d/",  : 
  Gone (HTTP 410).
Calls: google_form -> <Anonymous> -> read_html.response -> <Anonymous>
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      5.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
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'.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.1Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  13.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bin   5.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   1.2Mb
prime.factor: no visible global function definition for 'data'
prime.factor: no visible binding for global variable 'primlist'
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'quickstart.Rmd' using rmarkdown
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.5-23, (SVN revision 1121)
Geospatial Data Abstraction Library extensions to R successfully loaded
Loaded GDAL runtime: GDAL 3.2.1, released 2020/12/29
Path to GDAL shared files: D:/temp/Rtmpu4Y3gV/RLIBS_1ed74334b7caf/rgdal/gdal
GDAL binary built with GEOS: TRUE 
Loaded PROJ runtime: Rel. 7.2.1, January 1st, 2021, [PJ_VERSION: 721]
Path to PROJ shared files: D:/temp/Rtmpu4Y3gV/RLIBS_1ed74334b7caf/rgdal/proj
PROJ CDN enabled: FALSE
Linking to sp version:1.4-5
To mute warnings of possible GDAL/OSR exportToProj4() degradation,
use options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
Overwritten PROJ_LIB was D:/temp/Rtmpu4Y3gV/RLIBS_1ed74334b7caf/rgdal/proj
Warning in utils::download.file(url, tmp, quiet = TRUE) :
  URL 'https://www.lifewatch.be/sdmpredictors/sysdata.rda': status was 'SSL connect error'
trying URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
Content length 263 bytes
==================================================
Quitting from lines 79-91 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
cannot open URL 'http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif'
--- failed re-building 'quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible global function definition for 'dev.list'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
installed size is 61.6Mb
  sub-directories of 1Mb or more:
    doc      2.3Mb
    gdal     2.2Mb
    libs    44.0Mb
    proj     8.7Mb
    sqlite   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    www  16.5Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   8.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   1.3Mb
Package suggested but not available for checking: 'rPython'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.7Mb
    libs   1.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.2Mb
    libs   1.4Mb
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/4.2/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/4.2/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.3Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    help   1.7Mb
    libs   1.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    help   3.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.1Mb
    etc   1.3Mb
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Warning in fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (1.0.6)
than is installed on your system (1.0.7). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at 
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
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: 'rcytoscapejs'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      1.1Mb
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde: no visible global function definition for 'quantile'
stkde: no visible global function definition for 'heat.colors'
stkde: no visible global function definition for 'par'
stkde: no visible global function definition for 'image'
stkde: no visible global function definition for 'contour'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
stkde.sig: no visible global function definition for 'quantile'
stkde.sig: no visible global function definition for 'heat.colors'
stkde.sig: no visible global function definition for 'par'
stkde.sig: no visible global function definition for 'image'
stkde.sig: no visible global function definition for 'contour'
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.3Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc  10.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Running examples in 'svyPVpack-Ex.R' failed
The error most likely occurred in:

> ### Name: svyPVquantile
> ### Title: Quantile estimation
> ### Aliases: svyPVquantile
> ### Keywords: quantile
> 
> ### ** Examples
> 
> data(svy_example1)
> 
> erg_q <- svyPVquantile(by = ~ sex, svydat=svy.exrep,
+ pvs=c("plaus1","plaus2","plaus3"), quantile=c(0.2,0.7))
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Warning in svyquantile.svyrep.design(data, design[byfactor %in% byfactor[i],  :
  Jackknife replicate weights may not give valid standard errors for quantiles
Error in dimnames(x) <- dn : 
  length of 'dimnames' [2] not equal to array extent
Calls: svyPVquantile -> pv_quantile -> lapply -> FUN -> colnames<-
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in 'tab-Ex.R' failed
The error most likely occurred in:

> ### Name: tabmedians.svy
> ### Title: Create Table Comparing Group Medians (for Complex Survey Data)
> ### Aliases: tabmedians.svy
> 
> ### ** Examples
> 
> # Create survey design object
> library("survey")
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

> design <- svydesign(
+   data = tabsvydata,
+   ids = ~sdmvpsu,
+   strata = ~sdmvstra,
+   weights = ~wtmec2yr,
+   nest = TRUE
+ )
> 
> # Compare median BMI by sex
> (medtable1 <- tabmedians.svy(BMI ~ Sex, design = design))
Error in abs(medians) : non-numeric argument to mathematical function
Calls: tabmedians.svy
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.0Mb
    telemac   1.0Mb
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    gdal   2.1Mb
    libs  45.4Mb
    proj   8.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc        1.2Mb
    libs       7.0Mb
    tessdata  14.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    2.9Mb
    libs   1.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
author.search: no visible binding for global variable 'na.omit'
reference.list: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    examples  12.4Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Running examples in 'TNRS-Ex.R' failed
The error most likely occurred in:

> ### Name: TNRS
> ### Title: Resolve plant taxonomic names
> ### Aliases: TNRS
> 
> ### ** Examples
> 
> {
+ #Take a subset of the testfile to speed up runtime                  
+ tnrs_testfile <- tnrs_testfile[1:20,]
+  
+ results <- TNRS(taxonomic_names = tnrs_testfile)
+   
+ # Inspect the results
+ head(results, 10)
+ }
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: TNRS ... .TNRS_base -> postForm -> .postForm -> <Anonymous> -> fun
Execution halted
Error(s) in re-building vignettes:
--- re-building 'TNRS_vignette.Rmd' using rmarkdown
Quitting from lines 30-50 (TNRS_vignette.Rmd) 
Error: processing vignette 'TNRS_vignette.Rmd' failed with diagnostics:
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
--- failed re-building 'TNRS_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    help   1.4Mb
    libs  12.1Mb
Package suggested but not available for checking: 'toscaData'
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Package suggested but not available for checking: 'TreeDistData'
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   6.2Mb
Running examples in 'tricolore-Ex.R' failed
The error most likely occurred in:

> ### Name: ColorKeySextant
> ### Title: Sextant Scheme Legend
> ### Aliases: ColorKeySextant
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKeySextant(center = prop.table(runif(3)),
+                            values = c('#01A0C6', '#B8B3D8', '#F11D8C',
+                                       '#FFB3B3', '#FFFF00', '#B3DCC3'),
+                            label_as = 'pct_diff', show_center = TRUE)
Error: geom_polygon requires the following missing aesthetics: x and y
Backtrace:
    x
 1. +-(function (x, ...) ...
 2. \-ggtern:::print.ggplot(x)
 3.   +-ggtern::ggplot_build(x)
 4.   \-ggtern:::ggplot_build.ggplot(x)
 5.     \-ggtern:::by_layer(function(l, d) l$compute_geom_1(d))
 6.       \-ggtern:::f(l = layers[[i]], d = data[[i]])
 7.         \-l$compute_geom_1(d)
 8.           \-ggplot2:::f(..., self = self)
 9.             \-ggplot2:::check_required_aesthetics(...)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'choropleth_maps_with_tricolore.Rmd' using rmarkdown
Quitting from lines 61-72 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
stat_sf requires the following missing aesthetics: geometry
--- failed re-building 'choropleth_maps_with_tricolore.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   1.1Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc     6.6Mb
    ubinc   2.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    shinyapp   3.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc         1.4Mb
    dummydata   1.4Mb
    libs        2.4Mb
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.8Mb
    libs     34.2Mb
    proj      5.0Mb
ubRacing : predCandidate: no visible global function definition for
  'predict'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'pchisq'
ubRacing : aux2.friedman.edit: no visible global function definition
  for 'qt'
ubRacing : aux.friedman.edit: no visible global function definition for
  'wilcox.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  't.test'
ubRacing : aux.ttest.edit: no visible global function definition for
  'p.adjust'
ubRacing : idFolds: no visible global function definition for
  'quantile'
ubRacing: no visible binding for global variable 'sd'
ubSmoteExs: no visible global function definition for 'runif'
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs  14.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.2/utf8.Rcheck/00install.out' for details.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
installed size is 55.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      2.2Mb
    libs     43.2Mb
    proj      8.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  URL 'https://rud.is/dl/embedded.json': status was 'SSL connect error'
Error in file(con, "r") : 
  cannot open the connection to 'http://rud.is/dl/embedded.json'
Calls: from_spec -> readLines -> file
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    help          1.3Mb
    htmlwidgets   6.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(vprr)
  > 
  > test_check("vprr")
  == Failed tests ================================================================
  -- Error (test_read_files.R:26:3): CTD files are read in accurately ------------
  Error: arguments imply differing number of rows: 18351, 2, 1
  Backtrace:
      x
   1. +-testthat::expect_warning(...) test_read_files.R:26:2
   2. | \-testthat:::quasi_capture(enquo(object), label, capture_warnings)
   3. |   +-testthat:::.capture(...)
   4. |   | \-base::withCallingHandlers(...)
   5. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. \-vprr::vpr_ctd_read(ctd_files, station_of_interest)
   7.   \-base::data.frame(...)
  -- Error (test_read_files.R:69:3): VPR autoid files are read in accurately -----
  Error: replacement has 2 rows, data has 517
  Backtrace:
       x
    1. +-testthat::expect_silent(...) test_read_files.R:69:2
    2. | \-testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. |   +-testthat:::.capture(...)
    4. |   | +-withr::with_output_sink(...)
    5. |   | | \-base::force(code)
    6. |   | +-base::withCallingHandlers(...)
    7. |   | \-base::withVisible(code)
    8. |   \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. \-vprr::vpr_autoid_read(...)
   10.   +-base::`$<-`(...)
   11.   \-base::`$<-.data.frame`(...)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 20 ]
  Error: Test failures
  Execution halted
Packages in Depends field not imported from:
  'lattice' 'latticeExtra' 'stringdist'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
ldknn.odds: no visible global function definition for 'glm'
ldknn.odds: no visible binding for global variable 'binomial'
ldknn.odds: no visible global function definition for 'coefficients'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
Error(s) in re-building vignettes:
--- re-building 'intro.Rmd' using rmarkdown
--- finished re-building 'intro.Rmd'

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

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
i `x$a2` is of type <logical>>.
i `y$a2` is of type <character>>.
--- failed re-building 'united_nations.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   2.4Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.2/x13binary.Rcheck/00install.out' for details.
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    libs          2.1Mb
Running examples in 'xpose4-Ex.R' failed
The error most likely occurred in:

> ### Name: simprazExample
> ### Title: Function to create files for the simulated prazosin example in
> ###   Xpose
> ### Aliases: simprazExample
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> od = setwd(tempdir()) # move to a temp directory
> (cur.files <- dir()) # current files in temp directory
[1] "pdf16be06f309cd" "xptab1"         
> 
> simprazExample(overwrite=TRUE) # write files
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'xptab1': Invalid argument
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: simprazExample -> writeTab -> cat -> file
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Running examples in 'zoon-Ex.R' failed
The error most likely occurred in:

> ### Name: ModuleArguments
> ### Title: ModuleArguments
> ### Aliases: ModuleArguments
> 
> ### ** Examples
> 
> ModuleArguments('Background')
Error in ModuleArguments("Background") : 
  URL for module does not exist: https://raw.githubusercontent.com/zoonproject/modules/master/R/Background.R
Execution halted
Namespaces in Imports field not imported from:
  'DT' 'shinydashboard'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rARPACK' 'sparseLDA'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gsubfn'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'testthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'hunspell'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'svglite'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Benchmarking'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'filehash'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lubridate' 'parallel' 'rsvg' 'scales'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Rdpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'lifecycle'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'fields' 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BayesFactor' 'GGally' 'Hmisc' 'WRS2' 'boot' 'car' 'dplyr' 'effects'
  'effsize' 'forcats' 'ggplot2' 'lm.beta' 'nlme' 'readr' 'robust'
  'sandwich' 'sjstats' 'tidyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'glmmTMB'
Namespaces in Imports field not imported from:
  'DBI' 'assertthat' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'stats' 'useful'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mathjaxr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'plyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'mixexp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'randomNames' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rsolnp' 'SuperLearner' 'future.apply' 'ggplot2' 'progressr' 'stats'
  'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'taxize'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'glue' 'promises' 'websocket'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'dplyr' 'gridExtra' 'plyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'kernlab'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shinyjs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'hms'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lazyeval' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'car' 'datasets' 'dplyr' 'ggplot2' 'plotly' 'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DescTools' 'HH' 'datasets' 'dplyr' 'rhandsontable' 'shiny'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'httr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'haven' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'AER' 'ChainLadder' 'ISLR' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pls'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'survival' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ggthemes' 'shinythemes' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'bannerCommenter' 'config' 'feather' 'here' 'knitr' 'log4r' 'ps'
  'rmarkdown' 'skimr' 'snakecase' 'testthat' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httr' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'purrr' 'shinyBS' 'shinydashboard' 'shinyjs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'gmm' 'graphics' 'sandwich' 'stats4' 'utils'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'arules' 'arulesViz' 'dplyr' 'methods' 'plotly' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dlnm' 'ggplot2' 'lubridate' 'mvmeta' 'pbs' 'tsModel'
  All declared Imports should be used.
Found the following significant warnings:
  wmm.c:428:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int)'} [-Wincompatible-pointer-types]
  wmm.c:429:2: warning: initialization of 'struct audio_instance * (*)(struct SEXPREC *, float,  int,  int)' from incompatible pointer type 'wmm_instance_t * (*)(struct SEXPREC *, float,  int,  int)' {aka 'struct wmm_instance * (*)(struct SEXPREC *, float,  int,  int)'} [-Wincompatible-pointer-types]
See 'P:/pkgcheck/CRAN/audio/audio.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'abind'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'broom' 'diptest' 'ggplot2' 'hexbin' 'moments'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Hmisc' 'broom' 'tibble' 'usethis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'igraph'
  All declared Imports should be used.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  'Figure1.png'
Namespace in Imports field not imported from: 'zoo'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'memoise'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'plotly' 'shinycssloaders'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'bslib' 'rclipboard' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'openssl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'jose' 'openssl'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httr' 'openssl'
  All declared Imports should be used.
Note: found 76 marked Latin-1 strings
  Note: found 62811 marked UTF-8 strings
Namespace in Imports field not imported from: 'glpkAPI'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tkrplot'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats4'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ranger'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mvnfast'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dotenv' 'dplyr' 'googleAuthR' 'httr' 'tibble' 'writexl'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'splines'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'circlize' 'hexbin' 'scales' 'sna'
  All declared Imports should be used.
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
   6.           \-BBmisc::stopf("Directory '%s' is not readable/writable!", path)
  -- Error (test_reduceResultsExperimentsParallel.R:169:3): reduceResultsExperimentsParallel applies on missing results --
  Error: Directory 'C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BatchExperiments/BatchExperiments.Rcheck/tests/testthat/unittests-files/unittest3c343fc52644/registry/reduceExperimentsParallel3c343bb62e81' is not readable/writable!
  Backtrace:
      x
   1. \-BatchExperiments::reduceResultsExperimentsParallel(...) test_reduceResultsExperimentsParallel.R:169:2
   2.   \-BatchJobs::batchMapQuick(...)
   3.     \-BatchJobs::makeRegistry(id = id, file.dir = file.dir, packages = packages)
   4.       \-BatchJobs:::makeRegistryInternal(...)
   5.         \-BatchJobs:::checkDir(...)
   6.           \-BBmisc::stopf("Directory '%s' is not readable/writable!", path)
  
  [ FAIL 4 | WARN 1 | SKIP 0 | PASS 178 ]
  Error: Test failures
  Execution halted
Running 'run-all.R'
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  sanitizePath(paths) not identical to cS(c(paths[1], dirname(tempdir()))).
  1/2 mismatches
  x[2]: "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BatchJobs/t
  x[2]: mp"
  y[2]: "P:/pkgcheck/CRAN/BatchJobs/tmp"
  -- Failure (test_sanitizePath.R:32:3): sanitizePath ----------------------------
  sanitizePath(path, make.absolute = TRUE, normalize.absolute = TRUE) not identical to cS(dirname(dirname(path))).
  1/1 mismatches
  x[1]: "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/BatchJobs/t
  x[1]: mp"
  y[1]: "P:/pkgcheck/CRAN/BatchJobs/tmp"
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 381 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'scales' 'utils'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/color.hpp
  src/stan_files/linear.hpp
  src/stan_files/reaction_time.hpp
  src/stan_files/success_rate.hpp
  src/stan_files/ttest.hpp
Some Unix compilers require LF line endings.
Error(s) in re-building vignettes:
--- re-building 'adaptation_level.Rmd' using rmarkdown
Loading required package: Rcpp

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

Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
Scale for 'y' is already present. Adding another scale for 'y', which will replace the existing scale.
--- finished re-building 'adaptation_level.Rmd'

--- re-building 'afterimages.Rmd' using rmarkdown
Loading required package: Rcpp

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

--- finished re-building 'afterimages.Rmd'

--- re-building 'flanker.Rmd' using rmarkdown
Loading required package: Rcpp

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

Quitting from lines 124-129 (flanker.Rmd) 
Error: processing vignette 'flanker.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building 'flanker.Rmd'

--- re-building 'stroop.Rmd' using rmarkdown
Loading required package: Rcpp
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
--- finished re-building 'stroop.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'magrittr' 'rstantools'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_bayesbr.h
Some Unix compilers require LF line endings.
Found the following Makefile(s) with CR or CRLF line endings:
  src/Makevars
Some Unix 'make' programs require LF line endings.
Namespaces in Imports field not imported from:
  'RcppParallel' 'rstantools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'MatrixModels'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RcppParallel' 'StanHeaders' 'astsa'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'RcppParallel' 'mlbench' 'rstantools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shinytest' 'testthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'FastGP'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'workflows'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'move'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'HDInterval' 'carData'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RcppNumerical'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'Matrix' 'matrixcalc' 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    2. \-bayestestR:::unupdate.blavaan(bfit)
    3.   +-base::suppressMessages(suppressWarnings(utils::capture.output(model_prior <- eval(cl))))
    4.   | \-base::withCallingHandlers(...)
    5.   +-base::suppressWarnings(utils::capture.output(model_prior <- eval(cl)))
    6.   | \-base::withCallingHandlers(...)
    7.   +-utils::capture.output(model_prior <- eval(cl))
    8.   | \-base::withVisible(...elt(i))
    9.   +-base::eval(cl)
   10.   | \-base::eval(cl)
   11.   \-blavaan::blavaan(...)
   12.     \-blavaan:::coeffun_stanmarg(...)
  
  [ FAIL 1 | WARN 8 | SKIP 11 | PASS 198 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_model.cc
  src/stanExports_model.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'ggfortify' 'ggplot2' 'matrixStats' 'reshape2' 'scales'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'locfit' 'secr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'latticeExtra' 'rgdal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'coda' 'knitr' 'plyr'
  All declared Imports should be used.
Package suggested but not available for checking: 'BRugs'
Namespaces in Imports field not imported from:
  'knitr' 'rlang'
  All declared Imports should be used.
Running examples in 'bcrypt-Ex.R' failed
The error most likely occurred in:

> ### Name: bcrypt
> ### Title: Bcrypt password hashing
> ### Aliases: bcrypt gensalt hashpw checkpw
> 
> ### ** Examples
> 
> # Secret message as a string
> passwd <- "supersecret"
> 
> # Create the hash
> hash <- hashpw(passwd)
Error: OpenSSL error in RAND_DRBG_instantiate: error retrieving entropy
Execution halted
Namespace in Imports field not imported from: 'DT'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rstantools'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/bs.hpp
  src/stan_files/ds.hpp
  src/stan_files/eds.hpp
  src/stan_files/fs.hpp
  src/stan_files/nse.hpp
  src/stan_files/sr.hpp
  src/stan_files/srs.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'Rcpp' 'chron' 'colorspace' 'gtable' 'htmltools' 'htmlwidgets'
  'httpuv' 'magrittr' 'munsell' 'plyr' 'scales' 'stringi' 'xtable'
  'yaml'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'htmltools' 'rstudioapi'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_bellreg.h
  src/stanExports_zibellreg.h
Some Unix compilers require LF line endings.
Running examples in 'benchr-Ex.R' failed
The error most likely occurred in:

> ### Name: benchmark
> ### Title: High Precise Measurement of R Expressions Execution Time
> ### Aliases: benchmark
> 
> ### ** Examples
> 
> ## Measure the time it takes to dispatch a simple function call
> ## compared to simply evaluating the constant NULL
> f <- function() NULL
> res <- benchmark(NULL, f(), times = 1000L)
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Error in benchmark(NULL, f(), times = 1000L) : 
  All timed evaluations were either smaller than the estimated 
                 timer error or zero. The most likely cause is a low resolution clock.
Execution halted
Running 'tinytest.R'
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("benchr")
  + }
  
  test-benchmark.R..............    0 tests    0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Error in benchr::benchmark(1 + 1, 2 + 2) : 
    All timed evaluations were either smaller than the estimated 
                   timer error or zero. The most likely cause is a low resolution clock.
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
Namespace in Imports field not imported from: 'BiDAG'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'compiler'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'dplyr' 'ggplot2' 'readxl' 'rlist' 'shinyBS' 'shinyWidgets'
  'shinydashboard' 'shinyjs' 'shinythemes' 'stringr' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'coda' 'splines'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'nycflights13'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'httr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lubridate'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gtools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'desc' 'lme4' 'mitml'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'spatstat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'doParallel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'corrgram' 'rpivotTable' 'shinyAce'
  All declared Imports should be used.
Running 'test_coda.R'
  Running 'test_continue.R'
  Running 'test_diag.R'
  Running 'test_invisibles.R'
  Running 'test_parallel.R'
Running the tests in 'tests/test_parallel.R' failed.
Last 13 lines of output:
  r4         0.9727933        NA       NA       NA       NA         NA      NA
  sigsq.eps  0.4176265        NA       NA       NA       NA         NA      NA
            Bulk_ESS Tail_ESS
  beta            10       10
  lambda          10       10
  r1              10       10
  r2              10       10
  r3              10       10
  r4              10       10
  sigsq.eps       10       10
  > closeAllConnections()
  > 
  > future::plan(strategy = future::multiprocess, workers=2)
  Error: Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: R Under development (unstable) (2021-07-14 r80619); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server x64 build 14393; hostname: FRODO)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'bkmrhat-vignette.Rmd' using knitr
For guided examples, go to 'https://jenfb.github.io/bkmr/overview.html'
Loading required package: coda
Diagnostics and parallel chain functioning for Bayesian kernel machine regression
Quitting from lines 41-54 (bkmrhat-vignette.Rmd) 
Error: processing vignette 'bkmrhat-vignette.Rmd' failed with diagnostics:
Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: R Under development (unstable) (2021-07-14 r80619); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server x64 build 14393; hostname: FRODO)
--- failed re-building 'bkmrhat-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'R6' 'knitr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/stanmarg.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' 'ggplot2' 'rhandsontable' 'shiny'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/BEKKMGARCH.hpp
  src/stan_files/CCCMGARCH.hpp
  src/stan_files/DCCMGARCH.hpp
  src/stan_files/forecastBEKK.hpp
  src/stan_files/forecastCCC.hpp
  src/stan_files/forecastDCC.hpp
  src/stan_files/pdBEKKMGARCH.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'coda'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'matrixcalc'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rgraphviz' 'fastDummies'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'e1071'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'HSAUR3' 'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'psychTools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'CCA' 'brainR' 'elasticnet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'profileModel'
  All declared Imports should be used.
Packages suggested but not available for checking: 'glmmADMB', 'glmmTMB'
Installation failed.
See 'P:/pkgcheck/CRAN/BRugs/BRugs.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'lifecycle'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rworldxtra' 'sp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mvtnorm' 'ssmn'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Hmisc' 'magrittr' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'qgraph' 'reshape2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'markdown'
  All declared Imports should be used.
Found the following significant warnings:
  w32-backend.c:24:5: warning: initialization of 'char **' from incompatible pointer type 'const char **' [-Wincompatible-pointer-types]
See 'P:/pkgcheck/CRAN/Cairo/Cairo.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'htmltools' 'shinydashboard'
  All declared Imports should be used.
Running examples in 'caracas-Ex.R' failed
The error most likely occurred in:

> ### Name: diag<-.caracas_symbol
> ### Title: Replace diagonal
> ### Aliases: diag<-.caracas_symbol
> 
> ### ** Examples
> 
> if (has_sympy()) {
+   A <- matrix(c("a", 0, 0, 0, "a", "a", "a", 0, 0), 3, 3)
+   B <- as_sym(A)
+   B
+   diag(B)
+   diag(B) <- "b"
+   B
+   diag(B)
+ }
Error in py_get_attr_impl(x, name, silent) : 
  AttributeError: MutableDenseMatrix has no attribute diagonal.

Detailed traceback:
  File "C:\Users\tomas\AppData\Local\basilisk\105CB4~1.2\0\lib\site-packages\sympy\matrices\matrices.py", line 2141, in __getattr__
    "%s has no attribute %s." % (self.__class__.__name__, attr))
Calls: diag ... py_get_attr_or_item -> py_get_attr -> py_get_attr_impl
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
    4. +-caracas::diag(B)
    5. \-caracas:::diag.caracas_symbol(B)
    6.   +-caracas::eval_to_symbol(x$pyobj$diagonal())
    7.   | \-base::grepl("[0-9-.]+/[0-9-.]+", x, perl = TRUE)
    8.   |   \-base::is.factor(x)
    9.   +-x$pyobj$diagonal
   10.   \-reticulate:::`$.python.builtin.object`(x$pyobj, "diagonal")
   11.     \-reticulate:::py_get_attr_or_item(x, name, TRUE)
   12.       \-reticulate::py_get_attr(x, name)
   13.         \-reticulate:::py_get_attr_impl(x, name, silent)
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 307 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'details'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Hmisc' 'methods' 'readr' 'recipes' 'sf' 'stringr' 'utils'
  All declared Imports should be used.
Running examples in 'caRpools-Ex.R' failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
>   
> data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
+ treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+ norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
+ mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)
Warning in system(mageckstring) : 'mageck' not found
Warning in file(file, "rt") :
  cannot open file 'TEST.gene_summary.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: stat.mageck -> load.file -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'CaRpools.Rmd' using rmarkdown
converting counts to integer mode
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Warning in DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Quitting from lines 1956-1959 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'CaRpools.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'animation' 'devtools' 'gapminder' 'knitr' 'rlist' 'rmarkdown'
  'roxygen2' 'sde' 'shiny' 'tidyverse' 'usethis' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'janitor' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'crayon' 'dplyr' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tidyverse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'broom' 'epitools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lubridate' 'tidyverse'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_simplexes.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'prettydoc'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_cbqb.h
  src/stanExports_cbqbv.h
  src/stanExports_cbqd.h
  src/stanExports_cbqdv.h
  src/stanExports_cbqfixb.h
  src/stanExports_cbqfixbv.h
  src/stanExports_cbqfixd.h
  src/stanExports_cbqfixdv.h
  src/stanExports_cbqpanelb.h
  src/stanExports_cbqpanelbv.h
  src/stanExports_cbqpaneld.h
  src/stanExports_cbqpaneldv.h
  src/stanExports_cbqrandomb.h
  src/stanExports_cbqrandombv.h
  src/stanExports_cbqrandomd.h
  src/stanExports_cbqrandomdv.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'GeneNet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fields'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'formula.tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggpubr' 'matrixStats' 'qlcMatrix'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'data.table'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'base' 'stats' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lmtest'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'bench' 'ggplot2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rappdirs' 'stringr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'generics'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gamlss.dist'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'forcats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'htmltools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'dplyr' 'prettydoc' 'rmdformats' 'skimr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'circlize'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RInside' 'circular'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shinyBS'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rpart'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fritools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'methods' 'purrr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'cluster' 'datasets' 'dplyr' 'klaR' 'psycho' 'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'FNN' 'R.utils' 'SearchTrees' 'colorspace' 'colourpicker'
  'data.table' 'fields' 'mapproj' 'maps' 'maptools' 'ncdf4' 'raster'
  'rworldxtra' 'shinyFiles' 'shinyjs' 'shinythemes' 'sp' 'tcltk'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'maptools' 'rgdal' 'rworldxtra'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'caret' 'e1071' 'epitools' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'htmltools' 'htmlwidgets' 'readxl' 'testthat' 'widgetframe'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'nnet'
  All declared Imports should be used.
Package required but not available: 'ggtern'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error(s) in re-building vignettes:
  ...
--- re-building 'codalm_quickstart.Rmd' using rmarkdown
Quitting from lines 63-69 (codalm_quickstart.Rmd) 
Error: processing vignette 'codalm_quickstart.Rmd' failed with diagnostics:
Initialization of plan() failed, because the test future used for validation failed. The reason was: Package 'future' is not installed on worker (r_version: R Under development (unstable) (2021-07-14 r80619); platform: x86_64-w64-mingw32 (64-bit); os: Windows Server x64 build 14393; hostname: FRODO)
--- failed re-building 'codalm_quickstart.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'graphics' 'jsonlite' 'rlang' 'tidyselect' 'vctrs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'readr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'yaml'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'coin' 'ggplot2' 'plyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'magrittr' 'qpdf'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'grid' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'crayon'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'chi' 'dplyr' 'spatstat.utils' 'utils'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/commonsMath/commonsMath.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'GGally' 'RColorBrewer' 'abind' 'diagram' 'ggplot2' 'grid' 'gtable'
  'igraph' 'magrittr' 'plyr' 'purrr' 'reshape2' 'scales' 'useful'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'PearsonDS' 'VGAM' 'actuar' 'fExtremes' 'rmutil'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'RcppArmadillo' 'base' 'lwgeom'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reshape'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/multiK.hpp
  src/stan_files/oneK.hpp
  src/stan_files/space_multiK.hpp
  src/stan_files/space_oneK.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'mcc'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'rmutil'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'ggplot2' 'rmarkdown' 'shinyWidgets' 'shinydashboard'
  'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'profr' 'xtable'
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
  Note: found 947 marked UTF-8 strings
Namespace in Imports field not imported from: 'jpeg'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'maps'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gstat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colourpicker' 'dplyr' 'markdown' 'shinyjs' 'table1' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mapview' 'plotly'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'gsl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'misc3d'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mediation'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'grDevices'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gdistance' 'raster'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'gbm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'igraph'
  All declared Imports should be used.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  -- Error (test-crm_links.R:55:3): crm_links: elife special handling ------------
  Error: res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
  Backtrace:
      x
   1. \-crminer::crm_links("10.7554/elife.04059") test-crm_links.R:55:2
   2.   \-crminer:::crm_works_links(dois = doi, ...)
   3.     +-stats::setNames(lapply(dois, get_links, ...), dois)
   4.     \-base::lapply(dois, get_links, ...)
   5.       \-crminer:::FUN(X[[i]], ...)
   6.         \-crminer:::crm_GET(sprintf("works/%s", x), NULL, FALSE, ...)
   7.           \-base::stopifnot(res$response_headers$`content-type` == "application/json;charset=UTF-8")
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'r6extended'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'dplyr' 'geosphere' 'mapdata' 'maps' 'marmap' 'shinydashboard'
  'shinyjs' 'stringr' 'swfscDAS'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'qte'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'extrafont' 'future'
  All declared Imports should be used.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  file.exists(tmp_metadata) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  -- 2. Error (test-metadata.R:48:5): External metadata loads automatically ------
  Error: invalid 'description' argument
  Backtrace:
   1. testthat::expect_identical(...) test-metadata.R:48:4
   4. base::readLines(dir(dirname(tmp), pattern = ".yaml", full.names = TRUE))
   5. base::file(con, "r")
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'epitools' 'rpivotTable' 'shinyMatrix'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pkgbuild'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/cov.hpp
  src/stan_files/ctsm.hpp
  src/stan_files/ctsmgen.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' 'party' 'rhandsontable' 'rpart'
  'rpart.plot' 'shiny'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pspearman'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rlang' 'tidyselect'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'titanic'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'plyr' 'simpleboot'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'fs' 'googleCloudStorageR'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gamlss'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'dashTable'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'miniUI'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'xml2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'future' 'iterators' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'rmarkdown' 'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'tidyverse' 'vctrs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'html5'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'lubridate' 'tseries'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'commonmark' 'htmltools' 'shinyhelper'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'CDM'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_dcpo.h
  src/stanExports_dcpo_kfold.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'MASS' 'qpdf'
  All declared Imports should be used.
'library' or 'require' call to 'UScensus2010' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'UScensus2010'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'JavaGD' 'OpenStreetMap' 'maptools' 'rgdal' 'scales' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: 'assertthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lattice'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/exact.hpp
  src/stan_files/exactsizes.hpp
  src/stan_files/lowrank.hpp
  src/stan_files/lowranksizes.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'tidyselect'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'datasets'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RColorBrewer'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'plyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'statmod' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'purrr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'sf' 'tidyverse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gplots'
  All declared Imports should be used.
Found the following significant warnings:
  digest.c:207:25: warning: too many arguments for format [-Wformat-extra-args]
  digest.c:432:25: warning: too many arguments for format [-Wformat-extra-args]
See 'P:/pkgcheck/CRAN/digest/digest.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'sandwich'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos' 'splancs' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'psych'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BiocManager' 'ggpubr' 'sna'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'readr'
  All declared Imports should be used.
Running examples in 'disdat-Ex.R' failed
The error most likely occurred in:

> ### Name: AWT
> ### Title: Australian Wet Tropics species distribution data
> ### Aliases: AWT
> ### Keywords: datasets
> 
> ### ** Examples
> 
> awt_po <- disPo("AWT")
> awt_bg <- disBg("AWT")
> 
> awt_pa_plant <- disPa("AWT", "plant")
> awt_env_plant <- disEnv("AWT", "plant")
> awt_pa_bird <- disPa("AWT", "bird")
> awt_env_bird <- disEnv("AWT", "bird")
> 
> 
> # Or all in one list
> awt <- disData("AWT")
Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match
Calls: disData -> do.call -> <Anonymous> -> rbind
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    8.   \-distill:::render_website(dir, "blog")
    9.     \-rmarkdown::render_site(dir)
   10.       \-generator$render(...)
   11.         \-distill:::render_collections(input, config, collections, quiet)
   12.           \-base::lapply(...)
   13.             \-distill:::FUN(X[[i]], ...)
   14.               \-distill:::render_collection(...)
   15.                 \-base::lapply(...)
   16.                   \-distill:::FUN(X[[i]], ...)
   17.                     \-distill:::render_collection_article(...)
   18.                       \-base::file.copy(...)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 3 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'dplyr' 'proxy'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggmulti' 'loon' 'loon.data' 'loon.ggplot' 'zenplots'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gridExtra' 'plotly' 'pryr' 'rpart'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggrepel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'GOstats' 'caTools' 'fdrtool'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gridExtra'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'DoseFinding' 'ggplot2' 'lattice' 'latticeExtra' 'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'parallel' 'rgdal' 'sp' 'tensorflow'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'tidyr' 'tidyverse'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  * empty test (1)
  
  == Failed tests ================================================================
  -- Error (test-decode.R:24:3): decoding URL works ------------------------------
  Error: Unable to decode triangular mesh data
  Backtrace:
      x
   1. +-testthat::expect_is(...) test-decode.R:24:2
   2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
   3. |   \-rlang::eval_bare(expr, quo_get_env(quo))
   4. \-dracor::draco_decode(carurl, quiet = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 6 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'magrittr' 'purrr' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'arm' 'car' 'dotwhisker' 'gapminder' 'ggeffects' 'ggthemes' 'gt'
  'interplot' 'kableExtra' 'knitr' 'likert' 'modelsummary' 'moments'
  'nnet' 'ordinal' 'performance' 'scales' 'summarytools' 'tibble'
  'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rJava' 'tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'digest' 'dplyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ncdf4' 'rgdal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'NatureSounds' 'av' 'magrittr' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'maptools' 'tools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'progress'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2' 'scales' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: 'rprojroot'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rappdirs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gtools' 'separationplot'
  All declared Imports should be used.
Error: package or namespace load failed for 'echarty':
 .onLoad failed in loadNamespace() for 'echarty', details:
  call: loadNamespace(x)
  error: there is no package called 'shiny'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Namespace in Imports field not imported from: 'pander'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich' 'urca'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rmisc' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dae' 'dplyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'magrittr' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'PCovR'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/indefficacy.hpp
  src/stan_files/nb.hpp
  src/stan_files/paired.hpp
  src/stan_files/simple.hpp
  src/stan_files/unpaired.hpp
  src/stan_files/zinb.hpp
  src/stan_files/zipaired.hpp
  src/stan_files/ziunpaired.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'snow'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'Rtsne' 'uwot'
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos'
  All declared Imports should be used.
Running examples in 'EnsemblePCReg-Ex.R' failed
The error most likely occurred in:

> ### Name: epcreg.save
> ### Title: Custom Functions for Disk I/O in 'EnsemblePCReg' Package
> ### Aliases: epcreg.save epcreg.load
> 
> ### ** Examples
> 
> data(servo)
> myformula <- class~motor+screw+pgain+vgain
> perc.train <- 0.7
> index.train <- sample(1:nrow(servo), size = round(perc.train*nrow(servo)))
> data.train <- servo[index.train,]
> data.predict <- servo[-index.train,]
> est <- epcreg(myformula, data.train, ncores=2
+   , baselearner.control=epcreg.baselearner.control(
+     baselearners="knn"
+     , baselearner.configs = make.configs("knn"
+       , config.df = expand.grid(kernel = "rectangular"
+         , k = c(5, 10)))), filemethod = TRUE)
running in parallel mode, using 2 cores
CV training of base learners...
binding predictions from all base learners...finished
finished CV training of base learners
processing fold 1 of 5 
processing fold 2 of 5 
processing fold 3 of 5 
processing fold 4 of 5 
processing fold 5 of 5 
> epcreg.save(est, "somefile")
> rm(est) # alternatively, exit and re-launch R session
> est.loaded <- epcreg.load("somefile")
Error in epcreg.load("somefile") : 
  unexpected multiple directories in tar filepaths
Execution halted
Namespaces in Imports field not imported from:
  'Biostrings' 'DECIPHER' 'ggplot2' 'reshape2' 'usethis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RCurl' 'bitops' 'rjson'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'SPECIES' 'ade4'
  All declared Imports should be used.
Found the following significant warnings:
  report.c:1466:31: warning: '%02d' directive writing between 2 and 11 bytes into a region of size between 1 and 8 [-Wformat-overflow=]
See 'P:/pkgcheck/CRAN/epanet2toolkit/epanet2toolkit.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'RSpectra' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'readr' 'tidyverse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tinytest'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'htmlwidgets'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ggplot2' 'knitr' 'pander'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httpuv' 'plyr' 'rgdal' 'rgeos' 'tidyverse' 'tokenizers'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'tidyselect' 'vctrs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'cubature' 'rootSolve'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'sna' 'statnet.common'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'signal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'rlang'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'matrixStats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'openxlsx' 'stringr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'readr' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'RColorBrewer' 'Rcpp' 'e1071' 'foreach' 'gam' 'ggplot2'
  'glmnet' 'nnet' 'polspline' 'repmis' 'splines' 'xgboost'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'numDeriv'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tsibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'forcats' 'formula.tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'caTools' 'httr' 'jsonlite' 'rlang'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RobustGaSP'
  All declared Imports should be used.
Found the following file(s) containing GNU extensions:
  inst/Rcgi/Makefile
  src/Rcgi/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'fdapace'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'usethis' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'ggplot2' 'randomcoloR' 'sqldf'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'e1071' 'lattice' 'randomForest' 'tibble' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'magrittr' 'testthat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rvest' 'stringi'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'prettycode'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'NlcOptim' 'usethis' 'xts'
  All declared Imports should be used.
Found the following significant warnings:
  fgsg.h:96:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:202:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:347:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:460:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:516:61: warning: passing argument 8 of 'dpotrs_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:636:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:717:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:852:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
  fgsg.h:996:41: warning: passing argument 5 of 'dpotrf_' from incompatible pointer type [-Wincompatible-pointer-types]
See 'P:/pkgcheck/CRAN/FGSG/FGSG.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'attempt' 'glue'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'yardstick'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_cnpmodelmcmc.cc
  src/stanExports_cnpmodelmcmc.h
  src/stanExports_getB0.cc
  src/stanExports_getB0.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'MASS' 'XML' 'gglasso' 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'curl' 'mathjaxr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'evaluate' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'paletteer'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'xtable'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RCurl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'kableExtra' 'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'stats' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'grid'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'dtplyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'decomposedPSF'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'blockCV' 'patchwork' 'proxy'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pkgKitten'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'tibble' 'viridis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'fable' 'fabletools' 'feasts' 'ggplot2' 'lubridate' 'tibble'
  'tidyr' 'tsibble' 'tsibbledata' 'urca'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'fRLR.Rnw'
  ...
   0.17    0.00    0.02 

> simpleLoop <- function() {
+     res = matrix(nrow = 0, ncol = 4)
+     for (i in 1:length(idx1)) {
+         mat = cbind(X[, idx1[i]], X[, idx2[i]] .... [TRUNCATED] 

> system.time(simpleLoop())

... incomplete output.  Crash?

  'fRLR.Rnw'... failed to complete the test
Package suggested but not available for checking: 'foba'
Namespaces in Imports field not imported from:
  'class' 'mlbench' 'neuralnet' 'rpart'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'foreach'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'geometry'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pROC' 'reshape2' 'survival'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'webshot'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'gamlss'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'functional' 'xts'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(GBcurves)
  > 
  > test_check("GBcurves")
  == Failed tests ================================================================
  -- Failure (test_gb.R:23:3): Test function -------------------------------------
  nrow(df.out) > 0 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 2 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'raster'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/gdalcubes/gdalcubes.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'badger'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rootSolve'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'survAUC'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'pracma' 'rlang'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'purrr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'repmis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Running examples in 'geno2proteo-Ex.R' failed
The error most likely occurred in:

> ### Name: generatingCDSaaFile
> ### Title: Generating a file containing the DNA and AA sequences of all the
> ###   protein coding regions (CDSs) in a genome
> ### Aliases: generatingCDSaaFile
> 
> ### ** Examples
> 
>     # the data folder in this package
>     dataFolder = system.file("extdata", package="geno2proteo") 
> 
>     geneticCodeFile_line = file.path(dataFolder, 
+                                     "geneticCode_standardTable_lines.txt")
>     gtfFile = file.path(dataFolder, 
+                 "Homo_sapiens.GRCh37.74_chromosome16_35Mlong.gtf.gz")
>     DNAfastaFile =  file.path(dataFolder, 
+             "Homo_sapiens.GRCh37.74.dna.chromosome.16.fa_theFirst3p5M.txt.gz")
>     
>     outputFolder = tempdir(); # using the current folder as output folder
>     # calling the function.
>     generatingCDSaaFile(geneticCodeFile_line=geneticCodeFile_line, 
+         gtfFile=gtfFile, DNAfastaFile=DNAfastaFile, outputFolder=outputFolder)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements
Calls: generatingCDSaaFile -> read.table -> scan
Execution halted
Running 'runTests.R'
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test_generatingCDSaaFile: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 7 elements
  ERROR in test_genomicLocsToWholeDNASequence: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
    line 2 did not have 13 elements
  
  Test files with failing tests
  
     test_functionsInGeno2proteo.R 
       test_generatingCDSaaFile 
       test_genomicLocsToWholeDNASequence 
  
  
  Error in BiocGenerics:::testPackage("geno2proteo") : 
    unit tests failed for package geno2proteo
  Execution halted
Errors in running code in vignettes:
when running code in 'geno2proteoIntroduction.Rnw'
  ...

> tmpFolder = tempdir()

> generatingCDSaaFile(geneticCodeFile_line = geneticCodeFile, 
+     gtfFile = gtfFile_chr16, DNAfastaFile = DNAfastaFile_chr16, 
+     outputFolder = .... [TRUNCATED] 

  When sourcing 'geno2proteoIntroduction.R':
Error: line 2 did not have 7 elements
Execution halted

  'geno2proteoIntroduction.Rnw'... failed
Error(s) in re-building vignettes:
  ...
--- re-building 'geno2proteoIntroduction.Rnw' using Sweave

Error: processing vignette 'geno2proteoIntroduction.Rnw' failed with diagnostics:
 chunk 3 (label = example_generatingCDSaaFile) 
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 7 elements

--- failed re-building 'geno2proteoIntroduction.Rnw'

SUMMARY: processing the following file failed:
  'geno2proteoIntroduction.Rnw'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building 'inspection.Rmd' using rmarkdown
Namespaces in Imports field not imported from:
  'maptools' 'rgdal' 'rgeos'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pander' 'readr' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'phonTools' 'rgdal' 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sf'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'readr' 'spatstat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'velociraptr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'dbplyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'iterators' 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RCurl' 'lubridate' 'readr' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'memoise' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pipeR' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'bitops' 'data.table' 'dplyr' 'httr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'scales' 'stringr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'XML'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'plotly'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'do' 'survival'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'GGEBiplotGUI' 'gge' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'grDevices' 'scales' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colorspace' 'grid' 'rstan'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'withr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'grDevices' 'gtable'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'mathjaxr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'Rdpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'productplots' 'scales'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'graph'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'sna' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'grid' 'scales'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gcookbook' 'ggthemes' 'moonBook' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'dplyr' 'glue' 'gridExtra' 'xts' 'zoo'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'grDevices'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'Formula' 'GGally' 'Hmisc' 'RPostgres' 'colourpicker' 'dplyr'
  'ggpmisc' 'ggpubr' 'ggrepel' 'gridExtra' 'markdown' 'plotly'
  'quantreg' 'rlang' 'shinyFiles' 'shinyjqui' 'shinyjs' 'survival'
  'survminer' 'table1' 'tidyr' 'zoo'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'randomForest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'nomogramFormula' 'survival'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'magrittr' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/ggtern/ggtern.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'class'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'refund'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lwgeom'
  All declared Imports should be used.
Running 'add-force.R'
  Running 'bare_repository.R'
  Running 'blame.R'
  Running 'blob.R'
  Running 'branch.R'
  Running 'bundle.R'
  Running 'checkout-named-branch.R'
  Running 'checkout.R'
  Running 'checkout_branch.R'
  Running 'checkout_commit.R'
  Running 'checkout_tag.R'
  Running 'clone_bare.R'
  Running 'clone_branch.R'
  Running 'clone_checkout.R'
  Running 'commit.R'
  Running 'commits_path.R'
  Running 'config.R'
  Running 'diff.R'
  Running 'fast_forward_merge.R'
  Running 'fetch.R'
  Running 'graph.R'
  Running 'index.R'
  Running 'invalid-conf-var.R'
  Running 'libgit2.R'
  Running 'ls_tree.R'
  Running 'merge.R'
  Running 'merge_named_branch.R'
  Running 'normal_merge.R'
  Running 'note.R'
  Running 'odb_blobs.R'
  Running 'pre-process-path.R'
Running the tests in 'tests/pre-process-path.R' failed.
Last 13 lines of output:
  List of 3
   $ staged   :List of 5
    ..$ new: chr "foo-1"
    ..$ new: chr "foo_dir/foo-2"
    ..$ new: chr "glob_dir/a.txt"
    ..$ new: chr "glob_dir/b.txt"
    ..$ new: chr "glob_dir/c.txt"
   $ unstaged : Named list()
   $ untracked:List of 2
    ..$ untracked: chr "foo-2"
    ..$ untracked: chr "glob_dir/d.md"
   - attr(*, "class")= chr "git_status"
  > stopifnot(identical(status_obs, status_exp))
  Error: identical(status_obs, status_exp) is not TRUE
  Execution halted
Namespaces in Imports field not imported from:
  'Rcpp' 'mockery'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shinyFiles'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mockery'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/glmmfields.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'AER' 'MASS' 'Matrix' 'censReg' 'effects' 'foreign' 'lme4' 'lmtest'
  'nnet' 'pBrackets' 'plm' 'pscl' 'sandwich'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Hmisc'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rhandsontable' 'shiny' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'assertthat' 'future' 'httr' 'jsonlite'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'intro.Rmd' using rmarkdown
Found GPG 2.2.19. Using keyring: C:\Users\tomas\AppData\Roaming\gnupg
Quitting from lines 89-91 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
GnuPG create key error: No agent running
--- failed re-building 'intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'Hmisc' 'RColorBrewer' 'agricolae' 'datasets' 'devtools' 'dplyr'
  'ggplot2' 'ggpubr' 'grid' 'gridGraphics' 'knitr' 'magrittr' 'pastecs'
  'rmarkdown' 'shinyWidgets' 'shinycssloaders'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'knitr' 'rmarkdown' 'spatstat.core'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'quadmesh'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'hutilscpp'
  All declared Imports should be used.
Running examples in 'grattan-Ex.R' failed
The error most likely occurred in:

> ### Name: rent_assistance
> ### Title: Rent assistance
> ### Aliases: rent_assistance
> 
> ### ** Examples
> 
> # current annual rent assistance
> rent_assistance()  
`fy.year` not set, so defaulting to fy.year = "2021-22"
Error: `fy.year = 2021-22` was not within the allowed range: 1999-00 <= fy.year <= 2020-21
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] 0 - 1 == -1
  -- Failure (test_youth_allowance.R:245:3): Partners (standard) -----------------
  length(...) not equal to 6L.
  1/1 mismatches
  [1] 0 - 6 == -6
  -- Failure (test_youth_allowance.R:251:3): Partners (standard) -----------------
  ...[] not equal to youth_allowance(...).
  Lengths differ: 1 is not 0
  -- Failure (test_youth_allowance.R:261:3): Partners (standard) -----------------
  ...[] not equal to youth_allowance(...).
  Lengths differ: 1 is not 0
  
  [ FAIL 9 | WARN 0 | SKIP 114 | PASS 773 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'mclust'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
Running 'testpage.R'
Running the tests in 'tests/testpage.R' failed.
Last 13 lines of output:
  > 
  > 
  > #######################################
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
    character string expected as first argument
  Calls: PostScriptTrace -> system
  Execution halted
Errors in running code in vignettes:
when running code in 'import.Rnw'
  ...
+   .... [TRUNCATED] 

> library("grImport")
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")

  When sourcing 'import.R':
Error: character string expected as first argument
Execution halted
when running code in 'importText.Rnw'
  ...
+     grid .... [TRUNCATED] 

> library(grImport)
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")

  When sourcing 'importText.R':
Error: character string expected as first argument
Execution halted

  'import.Rnw'... failed
  'importText.Rnw'... failed
Error(s) in re-building vignettes:
--- re-building 'import.Rnw' using Sweave
Loading required package: XML

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
  character string expected as first argument

--- failed re-building 'import.Rnw'

--- re-building 'importText.Rnw' using Sweave
Loading required package: XML

Error: processing vignette 'importText.Rnw' failed with diagnostics:
 chunk 4 (label = simpleimport) 
Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
  character string expected as first argument

--- failed re-building 'importText.Rnw'

SUMMARY: processing the following files failed:
  'import.Rnw' 'importText.Rnw'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'usethis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'msm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'rjags'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import 'mvtnorm::rmvnorm' by 'spam::rmvnorm' when loading 'growfunctions'
See 'P:/pkgcheck/CRAN/growfunctions/growfunctions.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'spgwr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'attempt' 'corpcor' 'glue' 'htmltools' 'pkgload' 'processx'
  'tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'gsubfn' 'stringr'
  All declared Imports should be used.
Found the following significant warnings:
  readstat/sas/readstat_sas.c:319:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1009:66: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1045:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1071:66: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1111:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1144:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/sas/readstat_sas7bdat_read.c:1248:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_read.c:129:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_read.c:140:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_por_write.c:64:52: warning: too many arguments for format [-Wformat-extra-args]
  readstat/spss/readstat_sav_write.c:1307:66: warning: '%d' directive output may be truncated writing between 1 and 10 bytes into a region of size 8 [-Wformat-truncation=]
  readstat/stata/readstat_dta_read.c:190:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:407:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:704:62: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:981:62: warning: too many arguments for format [-Wformat-extra-args]
See 'P:/pkgcheck/CRAN/haven/haven.Rcheck/00install.out' for details.
Found the following significant warnings:
  H5ls.c:78:73: warning: too many arguments for format [-Wformat-extra-args]
  H5ls.c:88:84: warning: too many arguments for format [-Wformat-extra-args]
See 'P:/pkgcheck/CRAN/hdf5r/hdf5r.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'MCMCpack' 'ggjoy' 'isotone' 'mvtnorm' 'questionr' 'rprojroot'
  'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'healthyR' 'healthyR.data' 'healthyR.ts'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'Matrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'purrr' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DiagrammeRsvg' 'Matrix' 'bookdown' 'captioner' 'rsvg'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'spatstat.linnet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MCMCpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'cubature' 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'here' 'readxlsb' 'usethis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'methods' 'rgl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'Rdpack'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'FactoMineR' 'dplyr' 'ggforce' 'ggplot2' 'lifecycle' 'purrr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_base.cc
  src/stanExports_base.h
  src/stanExports_base_logit.cc
  src/stanExports_base_logit.h
  src/stanExports_hs.cc
  src/stanExports_hs.h
  src/stanExports_hs_logit.cc
  src/stanExports_hs_logit.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'rvest' 'xml2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mapproj'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'xml2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colourpicker' 'shiny' 'wordcloud2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'magrittr' 'tidyr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/idem.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'kableExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'testit'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'expm' 'rlecuyer'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'kableExtra' 'knitr' 'xtable'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reticulate'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'covr' 'magrittr' 'roxygen2'
  All declared Imports should be used.
Found the following significant warnings:
  gies.cpp:793:12: warning: enumeration value 'SD_NONE' not handled in switch [-Wswitch]
See 'P:/pkgcheck/CRAN/IMaGES/IMaGES.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'keras'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'dplyr' 'haven'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- Failure (test_doIMRMCfromFile.R:45:7): doIMRMC given fileName does not change --
  `saveResult` not equal to `result`.
  Component "perReader": Component "readerID": 'current' is not a factor
  Component "perReader": Component "modalityA": 'current' is not a factor
  Component "perReader": Component "modalityB": 'current' is not a factor
  Component "Ustat": Component "modalityA": 'current' is not a factor
  Component "Ustat": Component "modalityB": 'current' is not a factor
  Component "Ustat": Component "UstatOrMLE": 'current' is not a factor
  Component "MLEstat": Component "modalityA": 'current' is not a factor
  Component "MLEstat": Component "modalityB": 'current' is not a factor
  Component "MLEstat": Component "UstatOrMLE": 'current' is not a factor
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'lme4' 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'optimr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'raster' 'sp'
  All declared Imports should be used.
Running 'tinytest.R'
Running the tests in 'tests/tinytest.R' failed.
Last 13 lines of output:
  test_utilities.R..............   10 tests [0;31m1 fails[0m 
  test_utilities.R..............   10 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   11 tests [0;31m1 fails[0m 
  test_utilities.R..............   12 tests [0;31m1 fails[0m 
  test_utilities.R..............   13 tests [0;31m1 fails[0m [0;34m18.0s[0m
  ----- FAILED[xcpt]: test_utilities.R<39--42>
   call| expect_error(moveDLL(quadfn, name = "testname", directory = tempdir(), 
   call| -->    unload = TRUE, overwrite = TRUE), "file can not be copied both 'from' and 'to'")
   diff| No error
  Error: 1 out of 30 tests failed
  Execution halted
Namespace in Imports field not imported from: 'ca'
  All declared Imports should be used.
Packages suggested but not available for checking: 'BGGM', 'glmmTMB'
Namespaces in Imports field not imported from:
  'DT' 'bsplus' 'colourpicker' 'kableExtra' 'markdown' 'shinyjs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stringr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'expm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'GlobalOptions' 'testthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'seqinr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mvtnorm' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
Running examples in 'IRATER-Ex.R' failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
[1] 0
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
[1] 0
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Namespaces in Imports field not imported from:
  'Rdpack' 'glmnet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'irr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colorRamps' 'virtualspecies'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'chemometrics'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'timereg'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'dplyr' 'magrittr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'fBasics' 'reshape' 'tidyr' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'ggExtra' 'ggplot2' 'grid' 'gridExtra' 'mcmcplots'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'GA'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ids'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BayesFactor' 'GGally' 'GPArotation' 'MASS' 'PMCMR' 'R6' 'ROCR'
  'afex' 'car' 'emmeans' 'ggridges' 'lavaan' 'multcomp' 'mvnormtest'
  'nnet' 'psych' 'vcd' 'vcdExtra'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'boot' 'fds' 'rpart'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Cairo' 'survC1'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'EQL' 'univariateML'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lme4' 'metafor' 'nlme'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'inline'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Biostrings' 'Rsamtools' 'rtracklayer'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fitdistrplus'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'SnowballC' 'stringi'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'FNN' 'caret' 'datasets' 'dplyr' 'e1071' 'psycho' 'rhandsontable'
  'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mice' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gmp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RUnit'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'callr' 'desc' 'parallel' 'repr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'utf8'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'SnowballC' 'beepr' 'broom' 'chinese.misc' 'dplyr' 'highcharter'
  'htmlwidgets' 'ldatuning' 'parallel' 'plotly' 'purrr' 'quanteda'
  'shinyBS' 'shinyWidgets' 'shinyalert' 'shinycssloaders' 'shinyjs'
  'stringr' 'textmineR' 'tidyr' 'tidytext' 'topicmodels'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'reticulate' 'tensorflow'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'shiny' 'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'htmlwidgets' 'jsonlite' 'sf'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'leaflet'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pracma' 'statmod'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: Python 'C:\Users\tomas\AppData\Local\basilisk\1.0.2\0\envs\r-reticulate\python.exe' was requested but 'C:/Users/tomas/AppData/Local/basilisk/1.0.2/0/python.exe' was loaded instead (see reticulate::py_config() for more information)
See 'P:/pkgcheck/CRAN/leiden/leiden.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'cli' 'glue' 'stringr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'knitr' 'purrr' 'rmarkdown'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RcppParallel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'jsonlite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'purrr' 'raster'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'M3C'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ddpcr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'SnowballC' 'data.table' 'e1071' 'fastmatch'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'knitr' 'pROC' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mnormt'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'nnls' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'checkmate'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'modules'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'distr'
  All declared Imports should be used.
Package in Depends field not imported from: 'logcondens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'value_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/lib/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type' {aka 'struct boost::container::dtl::pair<int, int>'} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'P:/pkgcheck/CRAN/lolog/lolog.Rcheck/00install.out' for details.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lpirfs)
  > 
  > test_check("lpirfs")
  Error in parse(con, n = -1, srcfile = srcfile, encoding = "UTF-8") : 
    test-diagnost_ols.R:19:8: unexpected $end
  18: 
  19: lm_modeÄ
             ^
  Calls: test_check ... doWithOneRestart -> force -> lapply -> FUN -> source_file -> parse
  Execution halted
Namespace in Imports field not imported from: 'lavaan'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Icens' 'interval'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rpostgis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ncdf4' 'raster'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'fs' 'progress'
  All declared Imports should be used.
Found the following significant warnings:
  lxb.c:62:25: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  lxb.c:62:21: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
See 'P:/pkgcheck/CRAN/lxb/lxb.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'e1071' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rlang' 'torch'
  All declared Imports should be used.
Package suggested but not available for checking: 'simpleaffy'
Namespaces in Imports field not imported from:
  'dplyr' 'googlesheets4' 'lifecycle' 'withr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'rmarkdown' 'testthat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gtools' 'reshape'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'rgdal' 'rlang' 'testthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 's2'
  All declared Imports should be used.
Note: found 16 marked Latin-1 strings
  Note: found 980 marked UTF-8 strings
Namespace in Imports field not imported from: 'betareg'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'bookdown' 'kableExtra' 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'kableExtra'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'effsize' 'psych'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'formatR' 'utf8'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'lars' 'methods' 'parallel' 'smoothmest'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'boot.heterogeneity'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'parallelMap' 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'FactoMineR' 'covr' 'curl' 'devtools' 'gh' 'git2r' 'grDevices' 'httr'
  'knitr' 'openssl' 'pkgbuild' 'rlang' 'rmarkdown' 'roxygen2'
  'spelling' 'testthat' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'glmnet'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'datasets' 'dplyr' 'psych' 'shiny'
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 2864 marked UTF-8 strings
Namespaces in Imports field not imported from:
  'patchwork' 'tidyverse' 'tm' 'wordcloud2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'ggplot2' 'lavaan'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'vroom'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'RColorBrewer' 'RODBC' 'dplyr' 'foreign' 'formattable' 'ggplot2'
  'haven' 'mem' 'openxlsx' 'plotly' 'readxl' 'shinyBS' 'shinyWidgets'
  'shinydashboard' 'shinyjs' 'shinythemes' 'stringi' 'stringr' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colourpicker' 'shinyBS' 'shinycssloaders'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'urca'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BiocStyle' 'Rgraphviz' 'fastAdaboost' 'graph' 'kernlab' 'klaR'
  'knitr' 'randomForest' 'reshape2' 'rpart' 'tools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pacman'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'e1071' 'gbm' 'ggplot2' 'graphics' 'randomForest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BiocManager' 'DT' 'GEOmetadb' 'RMySQL' 'RSQLite' 'gplots' 'pheatmap'
  'readr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lmerTest'
  All declared Imports should be used.
Running 'mpost.R'
Running the tests in 'tests/mpost.R' failed.
Last 13 lines of output:
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  > 
  > library(grImport)
  Loading required package: XML
  > PostScriptTrace("fig.1")
  Error in system(command, as.integer(flag), f, stdout, stderr, timeout) : 
    character string expected as first argument
  Calls: PostScriptTrace -> system
  Execution halted
Namespaces in Imports field not imported from:
  'ade4' 'dendextend' 'ggforce' 'ggrepel' 'stringr' 'tidyverse'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/AB_Emax.hpp
  src/stan_files/BNHM_Higgins.hpp
  src/stan_files/BNHM_Smith.hpp
  src/stan_files/Baseline_Emax.hpp
  src/stan_files/Beta_binomial.hpp
  src/stan_files/CBPlusBaseline_Emax.hpp
  src/stan_files/CB_Emax.hpp
  src/stan_files/Fix_Eff.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'ECoL'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'boot' 'energy'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MCMCpack' 'copula'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ggiraph' 'ggplot2' 'grid' 'gtools' 'scales' 'shinyBS'
  'shinyWidgets' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'GenomicAlignments' 'R.utils' 'data.table' 'magrittr' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'config' 'desc' 'dplyr' 'glue' 'withr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'AzureAuth' 'R6' 'curl' 'jsonlite' 'vctrs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'FactoMineR' 'softImpute'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DiceDesign' 'MaxPro' 'doSNOW' 'gmp' 'jpeg'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'markdown' 'metafor'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pracma' 'rstantools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mcmcr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ashr' 'fdrtool'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'R6'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DiscriMiner' 'MASS' 'caret' 'datasets' 'dplyr' 'e1071' 'klaR'
  'rhandsontable' 'shiny'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'randomForest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'data.table' 'e1071' 'mlr3' 'mlr3learners' 'mlr3measures' 'plyr'
  'purrr' 'ranger' 'readxl' 'shinyWidgets' 'shinyalert'
  'shinydashboard' 'shinyjs' 'shinythemes' 'stats' 'stringr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'QuantPsyc' 'corrgram' 'dplyr' 'forecast' 'psych' 'shinyAce'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'MM2Sdata.Rnw' using knitr
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MIKTEX~1.9\miktex\bin\x64\texify.exe" --quiet --pdf "MM2Sdata.tex" --max-iterations=20 -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/tex/latex" -I "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/rinst/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'MM2Sdata.Rnw' failed with diagnostics:
running 'texi2dvi' on 'MM2Sdata.tex' failed

LaTeX errors:
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153: pdfTeX error (font expan
sion): auto expansion is only possible with scalable fonts.
<argument> ...shipout:D \box_use:N \l_shipout_box 
                                                  \__shipout_drop_firstpage_...
l.153 ... 'citation("{}pkgname"{})'.}}\end{kframe}
.Rcheck/vign_test/MM2Sdata/vignettes/MM2Sdata.tex:153:  ==> Fatal error occurre
d, no output PDF file produced!

--- failed re-building 'MM2Sdata.Rnw'

SUMMARY: processing the following file failed:
  'MM2Sdata.Rnw'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'Cairo' 'DT' 'XML' 'caTools' 'data.table' 'dplyr' 'ggplot2'
  'htmltools' 'leaflet' 'lubridate' 'plotly' 'shinyjs' 'stringr' 'xts'
  'zoo'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'plotrix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'datasets' 'doParallel' 'parallel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'e1071' 'nnet' 'shiny' 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sads'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DALEX' 'DT' 'auditor' 'breakDown' 'drifter' 'svglite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'lattice'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'crayon' 'dials' 'glmnet' 'parsnip' 'progressr' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'crayon' 'dials' 'glue' 'parsnip'
  All declared Imports should be used.
Note: found 20506 marked Latin-1 strings
  Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: 'here'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ztable'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'international-mortality-tables-overview.Rmd' using rmarkdown
Quitting from lines 235-237 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
could not find function "whittaker"
--- failed re-building 'international-mortality-tables-overview.Rmd'

--- re-building 'using-the-mortalityTables-package.Rmd' using rmarkdown
Loading required package: ggplot2
--- finished re-building 'using-the-mortalityTables-package.Rmd'

SUMMARY: processing the following file failed:
  'international-mortality-tables-overview.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  'ggformula' 'magrittr' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'caret' 'ggformula' 'knitr' 'testthat' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggridges' 'ggstance'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'NlcOptim'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'moments' 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'datasets' 'grDevices' 'graphics' 'iterators' 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'capushe' 'shiny'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shape'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'polycor'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'cowsay'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ez'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'poweRlaw' 'rmutil'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'grDevices' 'knitr' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Kendall' 'perm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'glmnet' 'mlr3learners'
  All declared Imports should be used.
Running 'spelling.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   15. | \-dplyr:::check_grouped(.tbl, "mutate", "if")
   16. |   \-dplyr::is_grouped_df(tbl)
   17. +-dplyr::select(., Date, dplyr::everything())
   18. \-nationwider:::read_excel_silently(.)
   19.   +-base::suppressMessages(...)
   20.   | \-base::withCallingHandlers(...)
   21.   \-readxl::read_excel(..., na = c("", "N/A"))
   22.     \-readxl:::read_excel_(...)
   23.       +-readxl:::set_readxl_names(...)
   24.       | \-tibble::as_tibble(l, .name_repair = .name_repair)
   25.       \-readxl:::read_fun(...)
  
  [ FAIL 14 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'tuneR'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("nat.utils")
  Loading required package: nat.utils
  == Skipped tests ===============================================================
  * touch only supported on unix platforms (1)
  
  == Failed tests ================================================================
  -- Failure (test-fsutils.r:79:3): common_path works ----------------------------
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "P:/"
  y[1]: "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages"
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 73 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'caret' 'datasets' 'dplyr' 'e1071' 'rhandsontable' 'shiny'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'bookdown'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] 329 - 233 ==   96.2
  [2] 197 - 293 ==  -96.2
  [3] 208 - 336 == -128.2
  [4] 318 - 190 ==  128.2
  -- Failure (test-file-functions.R:62:2): grid mappings are read and applied ----
  latlon.data$y not equal to lat.dat[indices].
  4/4 mismatches (average diff: 28)
  [1] 49.5 - 12.4 ==  37.1
  [2] 49.5 - 12.4 ==  37.1
  [3] 40.4 - 59.1 == -18.8
  [4] 40.4 - 59.1 == -18.8
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 45 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'Deriv' 'compiler' 'stringi'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'fields' 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'igraph' 'rlang' 'tidyselect'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'downloader' 'jsonlite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'igraph'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'CoDiNA'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mgcv' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'xml2'
  All declared Imports should be used.
Running examples in 'nFCA-Ex.R' failed
The error most likely occurred in:

> ### Name: nfca
> ### Title: Numerical Formal Concept Analysis for Systematic Clustering
> ### Aliases: nfca
> 
> ### ** Examples
> 
> # View a build-in correlation matrix: nfca_example
> data("nfca_example", package = "nFCA")
> nfca_example
      H    W    S    D   HF   HM   WF   WM   H1   W1    O
1  1.00 0.95 0.90 0.90 0.85 0.85 0.80 0.80 0.40 0.30 0.10
2  0.95 1.00 0.88 0.88 0.70 0.70 0.87 0.87 0.20 0.45 0.15
3  0.90 0.88 1.00 0.82 0.80 0.80 0.76 0.76 0.10 0.10 0.02
4  0.90 0.88 0.82 1.00 0.82 0.82 0.81 0.81 0.10 0.10 0.05
5  0.85 0.70 0.80 0.82 1.00 0.95 0.65 0.65 0.08 0.06 0.01
6  0.85 0.70 0.80 0.82 0.95 1.00 0.60 0.60 0.06 0.07 0.01
7  0.80 0.87 0.76 0.81 0.65 0.60 1.00 0.95 0.03 0.05 0.01
8  0.80 0.87 0.76 0.81 0.65 0.60 0.95 1.00 0.01 0.02 0.01
9  0.40 0.20 0.10 0.10 0.08 0.06 0.03 0.01 1.00 0.02 0.01
10 0.30 0.45 0.10 0.10 0.06 0.07 0.05 0.02 0.02 1.00 0.02
11 0.10 0.15 0.02 0.05 0.01 0.01 0.01 0.01 0.01 0.02 1.00
>      
> # 1. using the default 'histogram' method and choosing threshold
> # automatically   
> nfca(data = nfca_example)
Warning in system("ruby multistagefca.rb") : 'ruby' not found
Warning in file.rename("example.dot", "example.txt") :
  cannot rename file 'example.dot' to 'example.txt', reason 'The system cannot find the file specified'
Warning in file(file, "rt") :
  cannot open file 'example.txt': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: nfca ... thresholdTEST -> as.matrix -> read.csv -> read.table -> file
Execution halted
Namespaces in Imports field not imported from:
  'rgdal' 'sp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rjson'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'deSolve'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'jsonlite'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiocManager'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'uroot'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'multicool'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lwgeom' 's2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'choroplethr' 'choroplethrMaps' 'data.table' 'forcats'
  'hurricaneexposure' 'plyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'crayon' 'digest' 'hash'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rJava'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'e1071' 'pROC' 'purrr' 'randomForest' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'e1071' 'glmnet'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'CAMAN' 'Hmisc' 'latexpdf' 'spatstat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rts'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'xgboost'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'Rdpack' 'base' 'graphics' 'parallel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'forecast' 'rlang' 'tsibble' 'viridis'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'oaih.Rnw'
  ...

> baseurl <- "http://epub.wu.ac.at/cgi/oai2"

> if (inherits(tryCatch(oaih_identify(baseurl), error = identity), 
+     "error")) q()
> proc.time()
   user  system elapsed 
   0.54    0.20   11.36 

... incomplete output.  Crash?

  'oaih.Rnw' using 'UTF-8'... failed to complete the test
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: 'bit64'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'units'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'e1071' 'ggthemes' 'mlbench'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'graphics'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gt'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_blrm_exnex.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'TCGAbiolinks' 'gdata' 'genefilter' 'maftools' 'readxl'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'e1071' 'fs' 'pdp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'safer'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'randomForest' 'ranger'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'dplyr' 'miniUI' 'text2vec'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/OpenCL/OpenCL.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'formattable' 'rintrojs' 'shinyBS' 'shinyFeedback' 'shinyWidgets'
  'shinycssloaders' 'shinydashboard' 'shinydashboardPlus' 'shinyjs'
  'shinythemes' 'splines' 'testthat' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'boot' 'splines'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'gridExtra' 'scales' 'tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'openssl'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'quantreg'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'flexsurv' 'nlme' 'tibble' 'tidyverse' 'tm'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'optparse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'trend'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'iterators'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rjson' 'rstudioapi'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'smoothmest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'caret' 'geoR' 'gstat' 'pryr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'survey'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'magrittr' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'flexsurv'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'logger'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'glue' 'logging' 'purrr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'KernSmooth' 'Mfuzz' 'SelectBoost' 'gplots' 'grid' 'jetset' 'magic'
  'msgps' 'splines' 'stats4' 'survival'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ade4'
  All declared Imports should be used.
Found the following significant warnings:
  putty/windows/winstore.c:665:38: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
  putty/windows/winstore.c:673:42: warning: passing argument 6 of 'RegQueryValueExA' from incompatible pointer type [-Wincompatible-pointer-types]
See 'P:/pkgcheck/CRAN/pbdRPC/pbdRPC.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'Matrix' 'pander'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fda'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/correlation.hpp
  src/stan_files/correlation_ll.hpp
  src/stan_files/factor.hpp
  src/stan_files/factor1.hpp
  src/stan_files/factor1_ll.hpp
  src/stan_files/factor_ll.hpp
  src/stan_files/unidim.hpp
  src/stan_files/unidim_adapt.hpp
  src/stan_files/unidim_ll.hpp
Some Unix compilers require LF line endings.
Running examples in 'pct-Ex.R' failed
The error most likely occurred in:

> ### Name: uptake_pct_govtarget
> ### Title: Calculate cycling uptake for UK 'Government Target' scenario
> ### Aliases: uptake_pct_govtarget uptake_pct_govtarget_2020
> ###   uptake_pct_godutch_2020 uptake_pct_ebike_2020
> ###   uptake_pct_govtarget_school2 uptake_pct_godutch_school2
> 
> ### ** Examples
> 
> distance = 15
> gradient = 2
> logit_pcycle = -3.959 + # alpha
+   (-0.5963 * distance) + # d1
+   (1.866 * sqrt(distance)) + # d2
+   (0.008050 * distance^2) + # d3
+   (-0.2710 * gradient) + # h1
+   (0.009394 * distance * gradient) + # i1
+   (-0.05135 * sqrt(distance) * gradient) # i2
> boot::inv.logit(logit_pcycle)
[1] 0.0107377
> uptake_pct_govtarget(15, 2)
[1] 0.0107377
> l = routes_fast_leeds
> pcycle_scenario = uptake_pct_govtarget(l$length, l$av_incline)
> pcycle_scenario_2020 = uptake_pct_govtarget_2020(l$length, l$av_incline)
> plot(l$length, pcycle_scenario, ylim = c(0, 0.2))
> points(l$length, pcycle_scenario_2020, col = "blue")
> 
> # compare with published PCT data:
> l_pct_2020 = get_pct_lines(region = "isle-of-wight")
Warning in CPL_read_ogr(dsn, layer, query, as.character(options), quiet,  :
  GDAL Error 1: SSL certificate problem: unable to get local issuer certificate
Error: Cannot open "https://github.com/npct/pct-outputs-regional-notR/raw/master/commute/lsoa/isle-of-wight/l.geojson"; The file doesn't seem to exist.
Execution halted
Running 'skip-heavy.R'
  Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == Failed tests ================================================================
  -- Error (test-get-pct.R:11:3): get_pct_ works ---------------------------------
  Error: Cannot open "https://github.com/npct/pct-outputs-regional-notR/raw/master/commute/lsoa/isle-of-wight/z.geojson"; The file doesn't seem to exist.
  Backtrace:
      x
   1. \-pct::get_pct_zones("isle-of-wight") test-get-pct.R:11:2
   2.   \-pct::get_pct(...)
   3.     \-sf::read_sf(u_file)
   4.       +-sf::st_read(...)
   5.       \-sf:::st_read.character(...)
   6.         \-sf:::CPL_read_ogr(...)
  
  [ FAIL 1 | WARN 1 | SKIP 1 | PASS 14 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'car' 'sandwich'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dvir' 'ibdsim2' 'paramlink2' 'pedbuildr' 'segregatr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'lhs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rms'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'jsonlite' 'memoise'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'future'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'intergraph'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'FrF2.catlg128'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'urltools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'Matrix' 'RColorBrewer' 'arm' 'epiDisplay' 'foreign' 'gbm'
  'grid' 'lattice' 'latticeExtra' 'lme4' 'nnet' 'parallel' 'splines'
  'survey' 'twang' 'xtable'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'PlackettLuce' 'StatRank' 'pmr' 'prefmod' 'rankdist'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'hexbin' 'quantreg'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'patchwork'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'stats'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ssh'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggrepel' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'plogr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'abc' 'doParallel' 'gdistance' 'geosphere' 'lhs' 'metRology' 'raster'
  'trend'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'car' 'lubridate'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'argonDash' 'argonR' 'colourpicker' 'ggplot2' 'grid' 'hexSticker'
  'png' 'shinyWidgets'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'regtools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'StanHeaders' 'dplyr' 'ggplot2' 'gridExtra' 'rstan' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ActCR' 'ActFrag' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rpart' 'withr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lmtest' 'sandwich'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'class' 'forcats' 'irr' 'lpSolve' 'purrr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shinycssloaders' 'shinythemes'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R.cache' 'docopt' 'here'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2/2 mismatches
  x[1]: "x <- function()\r\n"
  y[1]: "x <- function()\n"
  
  x[2]: "  NULL\r\n"
  y[2]: "  NULL\n"
  Backtrace:
      x
   1. +-withr::with_dir(...) test-hook-roxygenize.R:7:2
   2. | \-base::force(code)
   3. \-testthat::expect_equal(extract_diff_root("."), add_trailing_linebreak(text2)) test-hook-roxygenize.R:31:6
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 55 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'TH.data' 'moonBook'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ROCR' 'adabag' 'colourpicker' 'e1071' 'flexdashboard' 'glmnet'
  'kknn' 'neuralnet' 'plyr' 'randomForest' 'rattle' 'rpart' 'shinyAce'
  'shinyWidgets' 'shinydashboardPlus' 'shinyjs' 'tidyverse' 'xgboost'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'pkgdown' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'datasets' 'dplyr' 'psycho' 'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'curl' 'lubridate'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'tidyr' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'exactextractr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'rio' 'shiny' 'shinyjs' 'utils' 'webp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'LaplacesDemon' 'epitools' 'rpivotTable' 'shiny' 'shinyMatrix'
  All declared Imports should be used.
Found the following sources/headers not terminated with a newline:
  src/libprofit/include/profit/config.h
Some compilers warn on such files.
Namespaces in Imports field not imported from:
  'MASS' 'optimx' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'StanHeaders' 'methods' 'rstantools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'grDevices'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'matrixcalc' 'tidyr' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'qpdf'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'forecast' 'knitr'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'seasonal.Rmd' using rmarkdown
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.

Attaching package: 'dplyr'

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

    collapse

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)'

Warning: <anonymous>: ... may be used in an incorrect context: '.fun(piece, ...)'

Quitting from lines 331-342 (seasonal.Rmd) 
Error: processing vignette 'seasonal.Rmd' failed with diagnostics:
task 1 failed - "object 'makeModel' not found"
--- failed re-building 'seasonal.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Backtrace:
      x
   1. \-PSPManalysis::PSPMequi(...)
  -- Error (test.04-PNAS2002_5bsind.R:3:1): (code run outside of `test_that()`) --
  Error: 
  Executable PNAS2002_5bsind.dll not found! Computation aborted.
  
  Backtrace:
      x
   1. \-PSPManalysis::PSPMind(...) test.04-PNAS2002_5bsind.R:3:0
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/powerp.hpp
  src/stan_files/powerps.hpp
  src/stan_files/powerpsbinary.hpp
Some Unix compilers require LF line endings.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/cma.hpp
  src/stan_files/phma.hpp
  src/stan_files/psma.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'data.table' 'itsadug' 'mgcv'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'kableExtra' 'readr' 'tidyverse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'devtools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rmarkdown' 'stats'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_qmixbf.h
  src/stanExports_qmixbfv.h
  src/stanExports_qmixbr.h
  src/stanExports_qmixbrv.h
  src/stanExports_qmixcf.h
  src/stanExports_qmixcr.h
Some Unix compilers require LF line endings.
Running 'qMRI-test.R'
Running the tests in 'tests/qMRI-test.R' failed.
Last 13 lines of output:
  +                    maskFile, TR = TR, TE = TE,
  +                    FA = FA, verbose = FALSE)
  > #
  > #  Estimate Parameters in the ESTATICS model
  > #
  > modelMPM <- estimateESTATICS(mpm, method = "NLR", verbose=FALSE)
  > #
  > #  smooth maps of ESTATICS Parameters
  > #
  > setCores(2, reprt = FALSE)
  > modelMPMsp1 <- smoothESTATICS(modelMPM,
  +                               kstar = 16,
  +                               alpha = 0.004,
  +                               patchsize=1,
  +                               verbose = FALSE)
Errors in running code in vignettes:
when running code in 'qMRI-Example.Rnw'
  ...

> modelMPM <- estimateESTATICS(mpm, method = "NLR", 
+     verbose = FALSE)

> setCores(2, reprt = FALSE)

> modelMPMQLsp1 <- smoothESTATICS(modelMPM, mpmData = extract(mpm, 
+     "ddata"), kstar = 16, alpha = 0.004, patchsize = 1, verbose = FALSE)

... incomplete output.  Crash?

  'qMRI-Example.Rnw'... failed to complete the test
Error(s) in re-building vignettes:
  ...
--- re-building 'qMRI-Example.Rnw' using Sweave
Loading required package: awsMethods

Use the function setCores() to change the number of CPU cores.
Namespaces in Imports field not imported from:
  'knitr' 'msm'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'MatrixModels'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'viridis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'SparseM'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MCMCpack' 'gridExtra' 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pracma' 'zoo'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'dplyr' 'lmerTest'
  All declared Imports should be used.
Package unavailable to check Rd xrefs: 'BRugs'
Namespaces in Imports field not imported from:
  'asd' 'cubature' 'data.table' 'ggplot2' 'multxpert' 'survival'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'comat' 'rgdal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Hmisc' 'car' 'dplyr' 'grid' 'gridExtra' 'knitr' 'lmerTest' 'tidyr'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    7.   \-radix:::render_website(dir, "blog")
    8.     \-rmarkdown::render_site(dir)
    9.       \-generator$render(...)
   10.         \-radix:::render_collections(input, config, collections, quiet)
   11.           \-base::lapply(...)
   12.             \-radix:::FUN(X[[i]], ...)
   13.               \-radix:::render_collection(...)
   14.                 \-base::lapply(...)
   15.                   \-radix:::FUN(X[[i]], ...)
   16.                     \-radix:::render_collection_article(...)
   17.                       \-base::file.copy(...)
  
  [ FAIL 1 | WARN 8 | SKIP 0 | PASS 3 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'qpdf' 'utf8'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Rcompadre'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Biobase' 'CGHbase'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'BiocManager' 'stringi' 'xml2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'dplyr' 'jsonlite' 'rgbif' 'rgdal' 'rgeos' 'sp' 'spThin'
  'spatstat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RJDBC'
  All declared Imports should be used.
Found the following significant warnings:
  datetime.c:724:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:725:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:763:3: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:971:6: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1115:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1116:2: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
  datetime.c:1199:7: warning: 'tzname' is deprecated: Only provided for source compatibility; this variable might not always be accurate when linking to UCRT. [-Wdeprecated-declarations]
See 'P:/pkgcheck/CRAN/RApiDatetime/RApiDatetime.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'deldir' 'lifecycle'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'bitops'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_gMAP.h
Some Unix compilers require LF line endings.
Found the following notes/warnings:
  Non-staged installation was used
See 'P:/pkgcheck/CRAN/Rblpapi/Rblpapi.Rcheck/00install.out' for details.
Found the following non-empty subdirectories of 'inst' also used by R:
  inst/libs
It is recommended not to interfere with package subdirectories used by
R.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/blpapi_versioninfo.h
Some Unix compilers require LF line endings.
Package suggested but not available for checking: 'ggtern'
Namespace in Imports field not imported from: 'RcppEigen'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'dplyr'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: Bad session key
  == Failed tests ================================================================
  -- Error (test-decrypt.r:69:3): Decryption with passphrase passthrough and armor works --
  Error: cannot open the connection
  Backtrace:
      x
   1. \-base::readLines("file2-decrypt.txt") test-decrypt.r:69:2
   2.   \-base::file(con, "r")
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'SingleCellExperiment' 'mclust'
  All declared Imports should be used.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of 'unsigned int[1]' [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of 'unsigned int[1]' [-Warray-bounds]
See 'P:/pkgcheck/CRAN/RDieHarder/RDieHarder.Rcheck/00install.out' for details.
Subdirectory 'src' contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
Found the following significant warnings:
  ./io/BufferedSocketWriter.hpp:102:27: warning: array subscript 4 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:103:27: warning: array subscript 5 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:104:27: warning: array subscript 6 is outside array bounds of 'long int [1]' [-Warray-bounds]
  ./io/BufferedSocketWriter.hpp:105:27: warning: array subscript 7 is outside array bounds of 'long int [1]' [-Warray-bounds]
See 'P:/pkgcheck/CRAN/rDotNet/rDotNet.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'DBI' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'SemiPar' 'caret' 'dplyr' 'scales'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pkgload' 'processx'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'knitr' 'textshaping'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Deriv'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("reinstallr")
  == Failed tests ================================================================
  -- Error (test_03_show_missing_packages.R:24:3): missing packages are found ----
  Error: trying to use CRAN without setting a mirror
  Backtrace:
      x
   1. \-reinstallr::show_missing_packages(path = testpath, repos = repo) test_03_show_missing_packages.R:24:2
   2.   \-reinstallr:::missing_packages(found_packages$package, ...)
   3.     \-utils::available.packages(...)
   4.       \-utils::contrib.url(repos, type)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 5 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'gWidgets2tcltk'
  All declared Imports should be used.
Running 'test-all.R'
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
      unlink(filesToDel, recursive = TRUE)
  })(pkgURL = dots[[1L]][[1L]], pkgTD = dots[[2L]][[1L]])
  Browse[1]> debug: untar(tarfile = tf, exdir = dirname(pkgTD))
  Browse[2]> /usr/bin/tar: P\:\\pkgcheck\\CRAN\\Require\\tmp\\RtmpmS6RHd\\file16d34559e2b16: Cannot open: No such file or directory
  /usr/bin/tar: Error is not recoverable: exiting now
  debug: filesToDel <- dir(pkgTD, recursive = TRUE, full.names = TRUE, 
      include.dirs = TRUE)
  Browse[2]> debug: filesToDel <- filesToDel[grep("^DESCRIPTION$", basename(filesToDel), 
      invert = TRUE)]
  Browse[2]> debug: unlink(filesToDel, recursive = TRUE)
  Browse[2]> Error from message(pkg, " dependencies not found on CRAN; perhaps incomplete description? On GitHub?") 
  Error in message(pkg, " dependencies not found on CRAN; perhaps incomplete description? On GitHub?") : 
    object 'pkg' not found
  Calls: test_pkg ... pkgDepArchive -> lapply -> FUN -> message -> .makeMessage -> lapply
  Execution halted
Namespace in Imports field not imported from: 'Rserve'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'RTriangle'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pkgload'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'iCluster'
  All declared Imports should be used.
Running 'ChecksumFile.R'
  Running 'GenericDataFile.R'
Running the tests in 'tests/GenericDataFile.R' failed.
Last 13 lines of output:
  Warning in system(cmd, intern = intern, wait = wait | intern, show.output.on.console = wait,  :
    running command 'C:\Windows\system32\cmd.exe /c mklink "P:/pkgcheck/CRAN/R.filesets/tmp/RtmpcRYkuh/1.2(a).txt" "C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/R.filesets/tmp/RtmpcRYkuh/copy/1.2(a).txt"' had status 1
  GenericDataFile:
  Name: 1.2(a)
  Tags: 
  Full name: 1.2(a)
  Pathname: C:/msys64/home/tomas/ucrt3/svn/ucrt3/r_packages/pkgcheck/CRAN/R.filesets/tmp/RtmpcRYkuh/copy/1.2(a).txt
  File size: 153 B (153 bytes)
  [1] TRUE
  > 
  > # Sanity checks
  > stopifnot(!isFile(dfL))
  > stopifnot(isFile(df))
  Error: isFile(df) is not TRUE
  Execution halted
Namespaces in Imports field not imported from:
  'prob' 'titanic'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'leaflet' 'pals' 'raster' 'sp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'crul'
  All declared Imports should be used.
Note: found 22 marked Latin-1 strings
  Note: found 1265 marked UTF-8 strings
Found the following significant warnings:
  RhpcMPI.c:112:28: warning: ' "' directive output may be truncated writing 2 bytes into a region of size between 1 and 4096 [-Wformat-truncation=]
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
  fakemaster.c:123:83: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4046 [-Wformat-truncation=]
  fakemaster.c:109:60: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4069 [-Wformat-truncation=]
  fakemaster.c:97:68: warning: '%s' directive output may be truncated writing up to 4095 bytes into a region of size 4061 [-Wformat-truncation=]
See 'P:/pkgcheck/CRAN/Rhpc/Rhpc.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'glue'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httr' 'remotes' 'rmarkdown' 'shiny'
  All declared Imports should be used.
Found the following significant warnings:
  RInside.cpp:169:12: warning: 'char* strncpy(char*, const char*, size_t)' specified bound 260 equals destination size [-Wstringop-truncation]
See 'P:/pkgcheck/CRAN/RInside/RInside.Rcheck/00install.out' for details.
Found the following sources/headers with CR or CRLF line endings:
  src/RInsideAutoloads.h
  src/RInsideEnvVars.h
Some Unix compilers require LF line endings.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile
  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 'P:/pkgcheck/CRAN/rJava/rJava.Rcheck/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. 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.
Namespace in Imports field not imported from: 'XLConnect'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
Found the following significant warnings:
  internal/hash.c:142:16: warning: too many arguments for format [-Wformat-extra-args]
See 'P:/pkgcheck/CRAN/rlang/rlang.Rcheck/00install.out' for details.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/LGT.hpp
  src/stan_files/S2GT.hpp
  src/stan_files/SGT.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'RCarb' 'rmarkdown' 'shinyjs'
  All declared Imports should be used.
Found the following significant warnings:
  parser.c:150:3: warning: enumeration value 'STRATNODENBR' not handled in switch [-Wswitch]
  parser.c:212:3: warning: enumeration value 'STRATNODENBR' not handled in switch [-Wswitch]
  parser.c:334:3: warning: enumeration value 'STRATTESTNBR' not handled in switch [-Wswitch]
  parser.c:543:3: warning: enumeration value 'STRATTESTNBR' not handled in switch [-Wswitch]
  parser.c:600:3: warning: enumeration value 'STRATTESTNBR' not handled in switch [-Wswitch]
See 'P:/pkgcheck/CRAN/rmumps/rmumps.Rcheck/00install.out' for details.
Found the following sources/headers with CR or CRLF line endings:
  src/lib/scotch_6.0.9/include/scotch.h
  src/lib/scotch_6.0.9/include/scotchf.h
  src/lib/scotch_6.0.9/src/libscotch/scotch.h
  src/lib/scotch_6.0.9/src/libscotch/scotchf.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'qtl'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'impute'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'bridgesampling' 'callr' 'extraDistr' 'psych' 'runjags'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DEoptimR' 'DT' 'PerformanceAnalytics' 'ggplot2' 'graphics'
  'gridExtra' 'methods' 'shinyjs' 'utils' 'xts'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'diptest' 'methods' 'viridis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httpuv' 'utils'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   1. \-roxygen2:::expect_equal_strings(out1$get_value("details"), exp_details) test-rd-includermd.R:179:2
   2.   \-testthat::expect_equal(s1, s2) C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\roxygen2\roxygen2.Rcheck\tests\testthat\helper-test.R:12:2
  
  [ FAIL 1 | WARN 0 | SKIP 13 | PASS 733 ]
  Error: Test failures
  In addition: Warning messages:
  1: In for (handler in handlers) { :
    closing unused connection 7 (P:\pkgcheck\CRAN\roxygen2\tmp\Rtmp2T7Jem\file143f0340e143e)
  2: In for (handler in handlers) { :
    closing unused connection 6 (P:\pkgcheck\CRAN\roxygen2\tmp\Rtmp2T7Jem\file143f04e2b4bc2)
  3: In for (handler in handlers) { :
    closing unused connection 5 (P:\pkgcheck\CRAN\roxygen2\tmp\Rtmp2T7Jem\file143f04ca2f0)
  4: In for (handler in handlers) { :
    closing unused connection 4 (P:\pkgcheck\CRAN\roxygen2\tmp\Rtmp2T7Jem\file143f01f6538f3)
  Execution halted
Namespaces in Imports field not imported from:
  'dplyr' 'testthat'
  All declared Imports should be used.
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1617:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'P:/pkgcheck/CRAN/RPostgreSQL/RPostgreSQL.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'ape' 'igraph'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'NatureSounds'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'lubridate' 'reshape2' 'tidyr'
  All declared Imports should be used.
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'P:/pkgcheck/CRAN/RSclient/RSclient.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'labelled'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'binman' 'httr'
  All declared Imports should be used.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'P:/pkgcheck/CRAN/Rserve/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for x64 is not available
File 'P:/pkgcheck/CRAN/Rserve/Rserve.Rcheck/Rserve/libs/x64/Rserve.dll':
  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', '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. 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.
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'P:/pkgcheck/CRAN/RSNNS/RSNNS.Rcheck/00install.out' for details.
Running 'rsolr_unit_tests.R'
Running the tests in 'tests/rsolr_unit_tests.R' failed.
Last 13 lines of output:
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  curl: (60) SSL certificate problem: unable to get local issuer certificate
  More details here: https://curl.se/docs/sslcerts.html
  
  curl failed to verify the legitimacy of the server and therefore could not
  establish a secure connection to it. To learn more about this situation and
  how to fix it, please visit the web page mentioned above.
  Error in download.file(url, dest, method = "curl", extra = "-L") : 
    'curl' call had nonzero exit status
  Calls: <Anonymous> ... maybeInstallSolr -> installSolr -> downloadSolr -> download.file
  Execution halted
Namespace in Imports field not imported from: 'h2o'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RSQLite' 'knitr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/bernoulli.hpp
  src/stan_files/binomial.hpp
  src/stan_files/continuous.hpp
  src/stan_files/count.hpp
  src/stan_files/jm.hpp
  src/stan_files/lm.hpp
  src/stan_files/mvmer.hpp
  src/stan_files/polr.hpp
Some Unix compilers require LF line endings.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\x86_64-w64-mingw32.static.posix\bin/ld.exe: file246e06e645dab.o:file246e06e645dab.cpp:(.text.startup+0x7a94): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
  C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\x86_64-w64-mingw32.static.posix\bin/ld.exe: file246e06e645dab.o:file246e06e645dab.cpp:(.text.startup+0x7aba): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
  C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\x86_64-w64-mingw32.static.posix\bin/ld.exe: file246e06e645dab.o:file246e06e645dab.cpp:(.text$_ZN3tbb8internal26task_scheduler_observer_v3D0Ev[_ZN3tbb8internal26task_scheduler_observer_v3D0Ev]+0x1d): undefined reference to `tbb::internal::task_scheduler_observer_v3::observe(bool)'
  C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\x86_64-w64-mingw32.static.posix\bin/ld.exe: file246e06e645dab.o:file246e06e645dab.cpp:(.text$_ZN3tbb10interface623task_scheduler_observerD1Ev[_ZN3tbb10interface623task_scheduler_observerD1Ev]+0x1d): more undefined references to `tbb::internal::task_scheduler_observer_v3::observe(bool)' follow
  collect2.exe: error: ld returned 1 exit status
  == Failed tests ================================================================
  -- Error (test_stan_functions.R:70:1): (code run outside of `test_that()`) -----
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      x
   1. \-rstan::expose_stan_functions(stanc_ret, rebuild = TRUE, verbose = TRUE) test_stan_functions.R:70:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/emax.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'loo'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/stap_bernoulli.hpp
  src/stan_files/stap_binomial.hpp
  src/stan_files/stap_continuous.hpp
  src/stan_files/stap_count.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2021-07-14 r80619)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=C                          
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_4.2.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httr' 'logger'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'stringr' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DescTools' 'MASS' 'gridExtra'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'memoise' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'rmarkdown'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/RWinEdt/RWinEdt.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'mgcv'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'shinybusy'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'httr' 'jsonlite'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'network'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pvclust'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'cowplot' 'ggplot2' 'ggridges' 'ggstance' 'jmvcore'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'stringi' 'stringr' 'tibble' 'tidyr' 'tidytext'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'pracma'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'pbapply' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'gbm'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'covr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rgdal' 'rgeos' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'fansi'
  All declared Imports should be used.
Package suggested but not available for checking: 'rsbml'
Namespaces in Imports field not imported from:
  'cluster' 'factoextra' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'FD'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'lavaan' 'psych' 'semPlot' 'semTools' 'shinyAce'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'grid' 'purrr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'geometries'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'kableExtra' 'tidyverse'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reactable'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'VGAM' 'data.table' 'ggdendro' 'gridExtra' 'knitr'
  'latticeExtra' 'msm' 'plotly' 'purrr' 'shinyBS' 'shinydashboard'
  'xtable'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'KGode' 'XML' 'ggplot2' 'gridExtra' 'mvtnorm' 'reshape2' 'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'scales' 'websocket'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shiny' 'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'CARE1' 'LCMCR' 'coda' 'conting' 'dga' 'future' 'ggplot2' 'ipc'
  'promises' 'reshape' 'shinycssloaders' 'testthat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'shiny'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/include/freetype/ftautoh.h
  src/include/freetype/ftcffdrv.h
  src/include/freetype/ftttdrv.h
  src/include/freetype/internal/ftdriver.h
  src/include/freetype/internal/ftpic.h
  src/include/freetype/ttunpat.h
  src/include/zconf.h
  src/include/zlib.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'KernSmooth' 'MASS' 'class' 'cluster' 'lattice' 'nnet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'qpdf'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'car' 'ggplot2' 'magrittr' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'grid'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'digest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'future' 'magrittr' 'purrr' 'rlang' 'utils'
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building 'MCSE.Rmd' using rmarkdown

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


Attaching package: 'kableExtra'

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

    group_rows

--- finished re-building 'MCSE.Rmd'

Warning in file(con, "r") :
  cannot open file 'P:\pkgcheck\CRAN\simhelpers\tmp\RtmpgfiFrR\filead147c287f7e': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
Namespace in Imports field not imported from: 'quadprog'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'jsonlite' 'readr' 'shinycssloaders' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rgeos' 'sp'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'metafor'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'crqa' 'plot3D'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'magrittr' 'psych' 'stringr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'data.table' 'dplyr' 'lubridate' 'rmarkdown' 'yaml'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'CompQuadForm' 'Hmisc' 'boot' 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'methods'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'viridisLite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'methods' 'rgeos'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiocStyle'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'raster' 'rlang' 'sp' 'usethis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'lgr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rlist'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gtools' 'reshape2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'devtools' 'rstudioapi'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Require'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gtable' 'rlang' 'testthat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'future' 'geosphere' 'lubridate' 'tidyverse' 'viridis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'irlba' 'knitr' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'SpatialEpi' 'dplyr' 'dygraphs' 'ggplot2'
  'htmlwidgets' 'knitr' 'leaflet' 'mapproj' 'maptools' 'rgdal' 'rgeos'
  'rmarkdown' 'shinyjs' 'spdep' 'xts'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'tibble' 'viridisLite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'doParallel' 'ggplot2' 'parallel'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'xcms'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'e1071' 'specmine.datasets'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'pdftools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'class' 'mlbench'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'batchtools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggridges'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'RColorBrewer' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sampling'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'extrafont' 'ggplot2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rdpack' 'car' 'knitr' 'lmtest' 'rmarkdown'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'spatstat' 'spatstat.data' 'spatstat.linnet' 'spatstat.sparse'
  'spatstat.utils' 'testthat'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sessioninfo'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/fit_model_gomp.hpp
  src/stan_files/fit_model_log.hpp
  src/stan_files/simulate_data_gomp.hpp
  src/stan_files/simulate_data_log.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'shinydashboard'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'stabledist'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'workflowsets' 'yardstick'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'iterators' 'methods' 'rgdal'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pander' 'readr' 'tidyselect'
  All declared Imports should be used.
Running examples in 'stars-Ex.R' failed
The error most likely occurred in:

> ### Name: st_warp
> ### Title: Warp (resample) grids in stars objects to a new grid, possibly
> ###   in an new coordinate reference system
> ### Aliases: st_warp
> 
> ### ** Examples
> 
> geomatrix = system.file("tif/geomatrix.tif", package = "stars")
> (x = read_stars(geomatrix))
stars object with 2 dimensions and 1 attribute
attribute(s):
               Min. 1st Qu. Median    Mean 3rd Qu. Max.
geomatrix.tif    74     107    123 126.765     132  255
dimension(s):
  from to  offset delta                refsys point values x/y
x    1 20 1841002   1.5 WGS 84 / UTM zone 11N  TRUE   NULL [x]
y    1 20 1144003  -1.5 WGS 84 / UTM zone 11N  TRUE   NULL [y]
sheared raster with parameters: -5 -5 
> new_crs = st_crs(4326)
> y = st_warp(x, crs = new_crs)
> plot(st_transform(st_as_sfc(st_bbox(x)), new_crs), col = NA, border = 'red')
> plot(st_as_sfc(y, as_points=FALSE), col = NA, border = 'green', axes = TRUE, add = TRUE)
> image(y, add = TRUE, nbreaks = 6)
> plot(st_as_sfc(y, as_points=TRUE), pch=3, cex=.5, col = 'blue', add = TRUE)
> plot(st_transform(st_as_sfc(x, as_points=FALSE), new_crs), add = TRUE)
> # warp 0-360 raster to -180-180 raster:
> r = read_stars(system.file("nc/reduced.nc", package = "stars"))
trying to read file: C:\msys64\home\tomas\ucrt3\svn\ucrt3\r_packages\pkgcheck\CRAN\stars\stars.Rcheck\stars\nc\reduced.nc
Error in CPL_read_gdal(as.character(x), as.character(options), as.character(driver),  : 
  file not found
Calls: read_stars ... is_big -> read_stars -> <Anonymous> -> CPL_read_gdal
Execution halted
Namespaces in Imports field not imported from:
  'Hmisc' 'corrgram' 'datasets' 'dplyr' 'psych' 'psycho' 'rpivotTable'
  'shiny'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gbm' 'ggfortify' 'tibble' 'tidyverse'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
Warning in file(con, "r") :
  cannot open file 'P:\pkgcheck\CRAN\steps\tmp\RtmpcpxyXz\filedf704c69502e': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   2.   \-stevedore:::tar_files(basename(file), dirname(file))
   3.     \-stevedore:::tar_safe(tmp, files, complex = TRUE, external_list = external_list)
   4.       \-stevedore:::tar_system(tarfile, files, ...)
  -- Error (test-util-tar.R:70:3): external list ---------------------------------
  Error: tar failed with status 128:
  /usr/bin/tar: Cannot connect to P: resolve failed
  Backtrace:
      x
   1. \-stevedore:::tar_files(letters[1:6], p, external_list = TRUE) test-util-tar.R:70:2
   2.   \-stevedore:::tar_safe(tmp, files, complex = TRUE, external_list = external_list)
   3.     \-stevedore:::tar_system(tarfile, files, ...)
  
  [ FAIL 6 | WARN 1 | SKIP 159 | PASS 3264 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'huge' 'readr' 'scales' 'shinyjs'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > # Since the tests are supposed to guarantee that the bundled version installed
  > # correctly, they are skipped.
  > if (!is_solaris()) {
  +   test_check("stockfish")
  + }
  == Failed tests ================================================================
  -- Failure (test-fish.R:12:3): engine works ------------------------------------
  engine$isready() is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 18 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: 'bnlearn'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ks'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'dbscan'
  All declared Imports should be used.
Found the following significant warnings:
  icu69/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 156 bytes from a string of length 156 [-Wstringop-truncation]
See 'P:/pkgcheck/CRAN/stringi/stringi.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'broom' 'car' 'lmerTest' 'pbkrtest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'pls' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'UpSetR' 'alluvial' 'gridBase'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'bsplus' 'colourpicker' 'grDevices' 'graphics' 'jsonlite'
  'purrr' 'shinyWidgets' 'shinyjs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lwgeom' 'utf8'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'psych' 'referenceIntervals'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'backports' 'methods'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gridExtra' 'mvtnorm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'doParallel' 'pROC'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'learnr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/Exponential.hpp
  src/stan_files/Gamma.hpp
  src/stan_files/GenF.hpp
  src/stan_files/GenGamma.hpp
  src/stan_files/Gompertz.hpp
  src/stan_files/PolyWeibull.hpp
  src/stan_files/RP.hpp
  src/stan_files/WeibullAF.hpp
  src/stan_files/WeibullPH.hpp
  src/stan_files/logLogistic.hpp
  src/stan_files/logNormal.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'Rdpack' 'readr' 'rlang' 'survival' 'tidyverse' 'utils'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lubridate' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mapdata' 'utils'
  All declared Imports should be used.
Running examples in 'swissdd-Ex.R' failed
The error most likely occurred in:

> ### Name: get_geodata
> ### Title: Get Swiss Geodata
> ### Aliases: get_geodata
> 
> ### ** Examples
> 
> 
> # Get latest geodata at municipal level
> get_geodata()
Warning in CPL_get_layers(dsn, options, do_count) :
  GDAL Error 1: SSL certificate problem: self signed certificate in certificate chain
Cannot open data source https://www.bfs.admin.ch/bfsstatic/dam/assets/18124132/master
Error in CPL_get_layers(dsn, options, do_count) : Open failed.
Calls: get_geodata -> <Anonymous> -> CPL_get_layers
Execution halted
Running 'winpath.R'
Running the tests in 'tests/winpath.R' failed.
Last 13 lines of output:
  > trace(lazyRepo, stop)
  Tracing function "lazyRepo" in environment <namespace:switchr>
  Warning: Tracing only in the namespace; to untrace you will need:
  untrace("lazyRepo", where = getNamespace("switchr"))
  [1] "lazyRepo"
  attr(,"package")
  [1] "switchr"
  > install_packages("switchr", repos = defaultRepos(), lib = tmplib)
  caught error: Error: Bioconductor does not yet build and check packages for R version 4.2; see
    https://bioconductor.org/install
  
  Error in getStringType(repos) : 
    Got mixed string types (likely in seed). This shouldn't happen.
  Calls: install_packages -> install_packages -> getStringType
  Execution halted
Running examples in 'symengine-Ex.R' failed
The error most likely occurred in:

> ### Name: D,SymEngineDataType-method
> ### Title: Derivatives of a Symbolic Expression
> ### Aliases: D,SymEngineDataType-method
> 
> ### ** Examples
> 
> expr <- S(~ exp(x))
> D(expr) == expr
[1] TRUE
> expr <- S(~ x^2 + 2*x + 1)
> D(expr)
Error(s) in re-building vignettes:
  ...
--- re-building 'odesystem.Rmd' using rmarkdown
--- re-building 'quick_start.Rmd' using rmarkdown
SUMMARY: processing the following files failed:
  'odesystem.Rmd' 'quick_start.Rmd'

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: 'metR'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'gee' 'survival'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'stringr' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'devEMF' 'segmented' 'smoother' 'tools'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'jiebaR'
  All declared Imports should be used.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
   17.                 +-targets:::if_any(...)
   18.                 \-self$run_target(name)
   19.                   +-targets:::target_conclude(...)
   20.                   \-targets:::target_conclude.tar_builder(...)
   21.                     \-targets:::builder_conclude(target, pipeline, scheduler, meta)
   22.                       \-targets:::builder_wait_correct_hash(target)
   23.                         +-targets:::store_ensure_correct_hash(target$store, storage, deployment)
   24.                         \-targets:::store_ensure_correct_hash.tar_store_file(...)
   25.                           +-targets:::if_any(...)
   26.                           \-targets:::assert_path(store$file$path)
   27.                             \-targets:::throw_validate(...)
  
  [ FAIL 7 | WARN 0 | SKIP 8 | PASS 600 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'SnowballC' 'dplyr' 'igraph' 'tm' 'wordcloud2'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'drat' 'plyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RSQLite' 'duckdb' 'memoise'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'jsonlite' 'knitr' 'lazyeval' 'tidyr'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/taxlist/taxlist.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'Matrix' 'quadprog'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'colorspace' 'psych'
  All declared Imports should be used.
Package which this enhances but not available for checking: 'glmmTMB'
Namespace in Imports field not imported from: 'lexicon'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'doParallel' 'parallel' 'tidyr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggm'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'proxy'
  All declared Imports should be used.
Package suggested but not available for checking: 'gdalcubes'
Namespaces in Imports field not imported from:
  'crayon' 'purrr' 'readr'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/thurstonian_irt_model.hpp
  src/stan_files/thurstonian_irt_model_newdata.hpp
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  'grDevices' 'graphics' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mix'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Evomorph' 'cowplot' 'factoextra' 'gridExtra' 'lme4' 'lsr' 'plotly'
  'png' 'shapes'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'modeldata' 'workflowsets'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'janitor'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'brio' 'curl' 'diffobj' 'gitcreds' 'keyring' 'nlme' 'rgdal' 'stringi'
  'usethis' 'waldo'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dtplyr' 'googledrive' 'googlesheets4'
  All declared Imports should be used.
Installation failed.
See 'P:/pkgcheck/CRAN/tiledb/tiledb.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'cpp11' 'dplyr' 'magrittr' 'stringi'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'base64enc'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'geojsonsf' 'lwgeom'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'cowplot' 'ggplot2' 'jsonlite'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rappdirs' 'withr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'fs' 'stringr' 'torch' 'torchvision' 'zip'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'jmvcore'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'V8' 'colorspace'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'jpeg' 'pastecs' 'plyr' 'raster'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'neuralnet'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tree'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'boot' 'chron' 'randtoolbox'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/AugBin2T1A.hpp
  src/stan_files/BebopInPeps2.hpp
  src/stan_files/CrmEmpiricNormalPrior.hpp
  src/stan_files/CrmOneParamLogisticGammaPrior.hpp
  src/stan_files/CrmOneParamLogisticNormalPrior.hpp
  src/stan_files/CrmTwoParamLogisticNormalPrior.hpp
  src/stan_files/EffTox.hpp
  src/stan_files/NeuenschwanderTwoParamLogit.hpp
  src/stan_files/ThallHierarchicalBinary.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'gsrsb'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'countrycode' 'haven' 'readstata13' 'stringr' 'tibble' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ez' 'forcats' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tseries'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'crosstalk'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'EMD' 'vars'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'forecastHybrid'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'shinyAce' 'shinyjs'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'latticeExtra'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_colext.cc
  src/stanExports_colext.h
  src/stanExports_single_season.cc
  src/stanExports_single_season.h
Some Unix compilers require LF line endings.
Running 'aunitizer.R'
  Running 'runtt.R'
Running the tests in 'tests/runtt.R' failed.
Last 13 lines of output:
  
  v |  15       | Unitize 2 [22.3 s]
  
  / |   0       | testthat.zzrunlast                                              ALL TESTS COMPLETED!
  
  == Results =====================================================================
  Duration: 161.2 s
  
  -- Skipped tests  --------------------------------------------------------------
  * empty test (4)
  * fails CRAN (2)
  
  [ FAIL 1 | WARN 15 | SKIP 6 | PASS 834 ]
  Error: Test failures
  Execution halted
Running 'test_non_interactive.R'
  Running 'test_ok.R'
  Running 'test_ok_group.R'
  Running 'test_ut_cmp.R'
Running the tests in 'tests/test_ut_cmp.R' failed.
Last 13 lines of output:
  +     ok(cmp_lines(ut_cmp_identical(as.integer(4), 4),
  +         '--- as.integer(4)',
  +         ' int 4',
  +         '+++ 4',
  +         ' num 4',
  +         NULL), "Equivalent objects do not, unlike ut_cmp_equal(). We also fall back to using str(), as print() will produce identical output")
  + }))
  # ut_cmp_identical:nogit
  ok - Identical objects return true
  ok - Equivalent objects do not, unlike ut_cmp_equal(). We also fall back to using str(), as print() will produce identical output
  > 
  > proc.time()
     user  system elapsed 
     0.39    0.20    2.23 
  # Looks like you failed 1 of 15 tests.
Namespaces in Imports field not imported from:
  'extraDistr' 'logitnorm' 'nakagami' 'tibble'
  All declared Imports should be used.
Running examples in 'unrtf-Ex.R' failed
The error most likely occurred in:

> ### Name: unrtf
> ### Title: Convert rtf Documents
> ### Aliases: unrtf
> 
> ### ** Examples
> 
> library(unrtf)
> text <- unrtf("https://jeroen.github.io/files/sample.rtf", format = "text")
No config directories. Searched: ../share/
Error: System call to 'unrtf' failed
Execution halted
Namespaces in Imports field not imported from:
  'lavaan' 'lifecycle' 'patchwork' 'ragg' 'scales' 'simstandard'
  All declared Imports should be used.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'foreign' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: 'cli'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RCurl' 'stringdist' 'utils'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'rio'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'Cairo'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'car' 'rlang' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rcpp' 'foreach' 'iterators' 'maps' 'spam'
  All declared Imports should be used.
Package required but not available: 'taxlist'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespaces in Imports field not imported from:
  'plotrix' 'sp' 'viridis'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'mclust' 'rlang'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'sqldf'
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  src/stan_files/visit.hpp
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'parcats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'colorspace' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'glue' 'tidyr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Hmisc' 'XML' 'checkmate' 'gstat' 'intervals'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'EnvStats' 'shiny' 'stats'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lubridate' 'tibble'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'ENMeval' 'RColorBrewer' 'dismo' 'dplyr' 'jsonlite'
  'leaflet.extras' 'raster' 'rgdal' 'rgeos' 'rmarkdown' 'shinyjs'
  'shinythemes' 'sp' 'spThin' 'spocc' 'zip'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'WRS2' 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'flextable'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'rgdal' 'vctrs'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'zoo'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'lemon' 'tidyverse'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'httr' 'jsonlite'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tools'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shiny' 'tidyselect'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'here' 'rgeos' 'tibble'
  All declared Imports should be used.
Found the following significant warnings:
  trace_back_backtrace.c:87:19: warning: too many arguments for format [-Wformat-extra-args]
See 'P:/pkgcheck/CRAN/winch/winch.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'drc' 'imputeTestbench'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'DT' 'DescTools' 'HydeNet' 'RBGL' 'Rgraphviz' 'arules' 'bnlearn'
  'dplyr' 'graph' 'igraph' 'linkcomm' 'missRanger' 'parallel' 'psych'
  'rhandsontable' 'rintrojs' 'shinyBS' 'shinyWidgets' 'shinyalert'
  'shinycssloaders' 'shinydashboard' 'tools' 'visNetwork'
  All declared Imports should be used.
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Namespaces in Imports field not imported from:
  'fdadensity' 'locfit' 'locpol' 'modeest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'magrittr'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'simts'
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See 'P:/pkgcheck/CRAN/x13binary/x13binary.Rcheck/00install.out' for details.
Running 'testthat.R'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > if (!is_solaris) {
  +   test_check("xml2")
  + }
  This is libxml2 version 2.9.10 
  == Skipped tests ===============================================================
  * On CRAN (3)
  
  == Failed tests ================================================================
  -- Failure (test-write_xml.R:6:3): write_xml errors for incorrect directory and with invalid inputs --
  `write_xml(x, filename)` did not throw an error.
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 398 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  'qpdf' 'rlang' 'tibble'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggdendro'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'miniUI' 'shinyBS'
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building 'introduction-to-ymlthis.Rmd' using rmarkdown
Quitting from lines 175-177 (introduction-to-ymlthis.Rmd) 
Error: processing vignette 'introduction-to-ymlthis.Rmd' failed with diagnostics:
'"pandoc-citeproc"' not found
--- failed re-building 'introduction-to-ymlthis.Rmd'

--- re-building 'yaml-fieldguide.Rmd' using rmarkdown
Loading required namespace: roxygen2
i Loading ymlthis
--- finished re-building 'yaml-fieldguide.Rmd'

--- re-building 'yaml-overview.Rmd' using rmarkdown
--- finished re-building 'yaml-overview.Rmd'

SUMMARY: processing the following file failed:
  'introduction-to-ymlthis.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_ypbp.h
  src/stanExports_ypbp2.h
Some Unix compilers require LF line endings.
Found the following sources/headers with CR or CRLF line endings:
  src/RcppExports.cpp
  src/stanExports_yppe.h
  src/stanExports_yppe2.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: 'ghyp'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ggplot2' 'testthat'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'lubridate'
  All declared Imports should be used.
Package suggested but not available for checking: ‘BiocInstaller’
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(balance)
  > 
  > test_check("balance")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compute.R:3:1): (code run outside of `test_that()`) ─────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-compute.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-output.R:3:1): (code run outside of `test_that()`) ──────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-output.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-sort.R:3:1): (code run outside of `test_that()`) ────────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-sort.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-wide2long.R:3:1): (code run outside of `test_that()`) ───────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-wide2long.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blaise)
  > 
  > test_check("blaise")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_types.R:164:3): empty STRING ──────────────────────────────────
  rep(NA_character_, 10) not equal to dfnew[["A"]].
  Lengths differ: 10 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 419 ]
  Error: Test failures
  Execution halted
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glance.Rchoice
> ### Title: Glance at a(n) Rchoice object
> ### Aliases: glance.Rchoice
> 
> ### ** Examples
> 
> library(Rchoice)
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
> 
> mod <- Rchoice(vs ~ mpg + hp + factor(cyl),
+                data = mtcars,
+                family = binomial("probit"))
> tidy(mod)
# A tibble: 5 × 5
  term         estimate std.error statistic p.value
  <chr>           <dbl>     <dbl>     <dbl>   <dbl>
1 constant       6.01      4.64     1.30      0.195
2 mpg           -0.0957    0.134   -0.716     0.474
3 hp            -0.0244    0.0214  -1.14      0.253
4 factor(cyl)6  -0.980     1.23    -0.797     0.426
5 factor(cyl)8  -6.39    938.      -0.00682   0.995
> glance(mod)
Error: 'getSummary.Rchoice' is not an exported object from 'namespace:Rchoice'
Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/cairoDevice.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7f1528361c30, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown

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: Removed 102 row(s) containing missing values (geom_path).
--- finished re-building ‘quickstart.Rmd’

--- re-building ‘slowstart.Rmd’ using rmarkdown
Using a cache at: /tmp/RtmpFU1Tt4
Downloading data from https://www.data.gouv.fr/fr/datasets/r/001aca18-df6a-45c8-89e6-f82d689e6c01
Quitting from lines 59-63 (slowstart.Rmd) 
Error: processing vignette 'slowstart.Rmd' failed with diagnostics:
transfer closed with outstanding read data remaining
--- failed re-building ‘slowstart.Rmd’

--- re-building ‘supported-countries.Rmd’ using rmarkdown
--- finished re-building ‘supported-countries.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [3s/4s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("crminer")
  Loading required package: crminer
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-crm_links.R:55:3): crm_links: elife special handling ────────────
  Error: res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
  Backtrace:
      █
   1. └─crminer::crm_links("10.7554/elife.04059") test-crm_links.R:55:2
   2.   └─crminer:::crm_works_links(dois = doi, ...)
   3.     ├─stats::setNames(lapply(dois, get_links, ...), dois)
   4.     └─base::lapply(dois, get_links, ...)
   5.       └─crminer:::FUN(X[[i]], ...)
   6.         └─crminer:::crm_GET(sprintf("works/%s", x), NULL, FALSE, ...)
   7.           └─base::stopifnot(res$response_headers$`content-type` == "application/json;charset=UTF-8")
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
  Error: Test failures
  Execution halted
Running examples in ‘DSSAT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_v_fmt
> ### Title: Adds variable format information to a tibble
> ### Aliases: add_v_fmt
> 
> ### ** Examples
> 
> 
> # Extract file path for sample ecotype file
> sample_eco_file <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
> 
> # Read sample ecotype file
> eco <- read_eco(sample_eco_file)
Error: '@ECO#  ECONAME.........  TBASE  TOPT ROPT   P20  DJTI  GDDE  DSGFT  RUE   KCAN  TSEN  CDAY' does not exist in current working directory ('/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DSSAT.Rcheck').
Execution halted
Found the following files/directories:
  ‘.Rprofile’
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ie2miscdata’
Package suggested but not available for checking: ‘BGGM’
Running examples in ‘IntCal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mix.curves
> ### Title: Build a custom-made, mixed calibration curve.
> ### Aliases: mix.curves
> 
> ### ** Examples
> 
> mix.curves()
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IntCal/extdata/mixed.14C': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: mix.curves -> write.table -> file
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘modistools-vignette.Rmd’ using rmarkdown
Quitting from lines 48-50 (modistools-vignette.Rmd) 
Error: processing vignette 'modistools-vignette.Rmd' failed with diagnostics:
Your requested timed out or the server is unreachable
--- failed re-building ‘modistools-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Dependence on R version ‘3.6.2’ not with patchlevel 0
Running ‘exporting-methods.R’ [3s/4s]
  Running ‘testthat.R’ [34s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rhmmer)
  > 
  > test_check("rhmmer")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-parse.R:11:3): read_tblout works ──────────────────────────────
  `read_tblout(tblout_file)` produced messages.
  ── Failure (test-parse.R:17:3): read_domtblout works ───────────────────────────
  `read_domtblout(domtblout_file)` produced messages.
  ── Failure (test-parse.R:27:3): files with no data do not fail ─────────────────
  `read_domtblout(empty_tblout_file)` produced messages.
  ── Failure (test-parse.R:28:3): files with no data do not fail ─────────────────
  `read_tblout(empty_domtblout_file)` produced messages.
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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. 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.
Running examples in ‘rvest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: google_form
> ### Title: Make link to google form given id
> ### Aliases: google_form
> ### Keywords: internal
> 
> ### ** Examples
> 
> google_form("1M9B8DsYNFyDjpwSK6ur_bZf8Rv_04ma3rmaaBiveoUI")
Error in read_html.response(httr::GET(paste0("https://docs.google.com/forms/d/",  : 
  Gone (HTTP 410).
Calls: google_form -> <Anonymous> -> read_html.response -> <Anonymous>
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Dependence on R version ‘3.6.3’ not with patchlevel 0
Package suggested but not available for checking: ‘rcytoscapejs’
Found the following files/directories:
  ‘XMIwords.txt’
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

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

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
ℹ `x$a2` is of type <logical>>.
ℹ `y$a2` is of type <character>>.
--- failed re-building ‘united_nations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘abess-guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address 384, cause 'memory not mapped'
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets  12.2Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    R  14.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Packages suggested but not available for checking: 'rsvg', 'AdhereRViz'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘qpAdm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ADMIXTOOLS programs required by admixr are not in your $PATH variable.
At the very least, the following programs should be available:
    qp3Pop, qpDstat, qpF4ratio, qpAdm, qpWave
Make sure to modify the $PATH variable in your .Renviron file so 
that it points to the directory containing the ADMIXTOOLS programs.

Quitting from lines 131-134 (qpAdm.Rmd) 
Error: processing vignette 'qpAdm.Rmd' failed with diagnostics:
'wget' call had nonzero exit status
--- failed re-building ‘qpAdm.Rmd’

--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ADMIXTOOLS programs required by admixr are not in your $PATH variable.
At the very least, the following programs should be available:
    qp3Pop, qpDstat, qpF4ratio, qpAdm, qpWave
Make sure to modify the $PATH variable in your .Renviron file so 
that it points to the directory containing the ADMIXTOOLS programs.

── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.2     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 132-133 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'wget' call had nonzero exit status
--- failed re-building ‘tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘qpAdm.Rmd’ ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    tutorials   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggseas’
Package suggested but not available for checking: ‘rsvg’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.5Mb
Package suggested but not available for checking: ‘ssh’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    test_v8    2.1Mb
    testdata   2.4Mb
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   7.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Package suggested but not available for checking: ‘qCBA’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Package suggested but not available for checking: ‘RWeka’
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Package required but not available: ‘seasonal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aweSOM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-101 (aweSOM.Rmd) 
Error: processing vignette 'aweSOM.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aweSOM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘RestRserve’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.4Mb
Running examples in ‘bagged.outliertrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: bagged.outliertrees
> ### Title: Bagged OutlierTrees
> ### Aliases: bagged.outliertrees
> 
> ### ** Examples
> 
> library(bagged.outliertrees)
> 
> ### example dataset with interesting outliers
> data(hypothyroid)
> 
> ### fit a Bagged OutlierTrees model
> model <- bagged.outliertrees(hypothyroid,
+   ntrees = 10,
+   subsampling_rate = 0.5,
+   z_outlier = 6,
+   nthreads = 1
+ )

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======                                                               |  10%Error in unserialize(socklist[[n]]) : error reading from connection
Calls: bagged.outliertrees ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Found the following files/directories:
  ‘core’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘balance.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 41-45 (balance.Rmd) 
Error: processing vignette 'balance.Rmd' failed with diagnostics:
there is no package called 'robCompositions'
--- failed re-building ‘balance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    1.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article4.Rnw’ using knitr
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BLE_Categorical.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Categorical.Rmd’

--- re-building ‘BLE_Ratio.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Ratio.Rmd’

--- re-building ‘BLE_Reg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_Reg.Rmd’

--- re-building ‘BLE_SRS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BLE_SRS.Rmd’

--- re-building ‘BLE_SSRS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 87-95 (BLE_SSRS.Rmd) 
Error: processing vignette 'BLE_SSRS.Rmd' failed with diagnostics:
cannot allocate vector of size 753.8 Mb
--- failed re-building ‘BLE_SSRS.Rmd’

--- re-building ‘BayesSampling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘BayesSampling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    help   1.3Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [24s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.11.1 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  ===== Monitors =====
  thin = 1: tau, betalpha
  ===== Samplers =====
  conjugate sampler (5)
    - tau
    - betalpha[]  (4 elements)
  RW sampler (10)
    - betalpha[]  (10 elements)
  thin = 1: tau, betalpha, sigma, eta
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (testthat.R:3:1): (code run outside of `test_that()`) ─────────────────
  Error: Failed to create the shared library. Run 'printErrors()' to see the compilation errors.
  
  Backtrace:
      █
   1. └─bcgam::bcgam(...) testthat.R:3:0
   2.   └─bcgam:::bcgam.fit(...)
   3.     └─nimble::compileNimble(gaus)
   4.       └─project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5.         └─cppProj$compileFile(compileList, showCompilerOutput)
   6.           └─nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7.             └─nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  [ FAIL 1 | WARN 1 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 143-145 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'batchelor', 'kBET', 'splatter', 'scater', 'lisi', 'dlfUtils'
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.0Mb
installed size is 136.2Mb
  sub-directories of 1Mb or more:
    include  136.2Mb
Running examples in ‘biglasso-Ex.R’ failed
The error most likely occurred in:

> ### Name: predict.biglasso
> ### Title: Model predictions based on a fitted 'biglasso' object
> ### Aliases: predict.biglasso coef.biglasso
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ## Logistic regression
> data(colon)
> X <- colon$X
> y <- colon$y
> X.bm <- as.big.matrix(X, backingfile = "")
> fit <- biglasso(X.bm, y, penalty = 'lasso', family = "binomial")
Error in structure(new.time - time, class = "proc_time") : 
  R_Reprotect: only -14 protected items, can't reprotect index -16
Calls: biglasso -> system.time -> structure
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

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

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

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), 
+                          outputFileName = tempfile(pattern = 
+                          "BigQuic_output_matrix", fileext = ".Bmat"),
+                          lambda = lambda, numthreads = 1, memory_size = 512, 
+                          seed = 1, use_ram = TRUE)

 *** caught segfault ***
address 2, cause 'memory not mapped'
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:

> ### Name: snp_fastImputeSimple
> ### Title: Fast imputation
> ### Aliases: snp_fastImputeSimple
> 
> ### ** Examples
> 
> bigsnp <- snp_attachExtdata("example-missing.bed")
> G <- bigsnp$genotypes
> G[, 2]  # some missing values
  [1] NA NA  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0  1  0  1  0
 [26]  0  0  0  0  1  0  1  0  0  0  0  1  0  1  0  0  0  0  0  0  0  0  0  1  0
 [51]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
 [76]  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0 NA
[101]  0  1  0  0  0  0  0  0  1  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0  0
[126]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  0  0  0 NA  0
[151]  1  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  1  0  0
[176]  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  0  0  1  0  0  1  0  0
> G2 <- snp_fastImputeSimple(G)

 *** caught segfault ***
address f8252000, cause 'invalid permissions'

Traceback:
 1: impute(Gna, method, ncores)
 2: snp_fastImputeSimple(G)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘bigstatsr-Ex.R’ failed
The error most likely occurred in:

> ### Name: asPlotlyText
> ### Title: Plotly text
> ### Aliases: asPlotlyText
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)

 *** caught segfault ***
address f8008000, cause 'invalid permissions'

Traceback:
 1: increment_scaled_tcrossprod(K, X_part_temp, X, ind.row, ind.col.ind,     ms$center, ms$scale)
 2: big_tcrossprodSelf(X, fun.scaling = fun.scaling, ind.row = ind.row,     ind.col = ind.col, block.size = block.size)
 3: DualBigPCA(X, fun.scaling, ind.row, ind.col, block.size, k)
 4: big_SVD(X, big_scale(), k = 10)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.4Mb
    extdata   1.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in ‘birdring-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw.recmap
> ### Title: Plot ringing data
> ### Aliases: draw.recmap
> ### Keywords: graphics
> 
> ### ** Examples
> 
> data(lancol)
> if (requireNamespace("rgeos", quietly=TRUE) && packageVersion("rgeos") >= "0.5.1") {
+   if (rgeos::get_RGEOS_CheckValidity() == 1L) rgeos::set_RGEOS_CheckValidity(2L)
+ }
> draw.recmap(lancol,lines=2,border='gray',subset="ring=='13B...6919'",gcircle=TRUE,zoom=3)
Error in RGEOSBinTopoFunc(spgeom1, spgeom2, byid, id, drop_lower_td, unaryUnion_if_byid_false,  : 
  TopologyException: Input geom 0 is invalid: Ring Self-intersection at or near point 23.325118450000002 43.886598820000003 at 23.325118450000002 43.886598820000003
Calls: draw.recmap -> lapply -> FUN -> gIntersection -> RGEOSBinTopoFunc
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Package suggested but not available for checking: ‘IHW’
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blaise)
  > 
  > test_check("blaise")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_types.R:164:3): empty STRING ──────────────────────────────────
  rep(NA_character_, 10) not equal to dfnew[["A"]].
  Lengths differ: 10 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 419 ]
  Error: Test failures
  Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE.FC
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE.FC REGE.FC.ow REGE REGE.ow REGE.for REGD.for REGE.ow.for
> ###   REGD.ow.for REGE.ownm.for REGE.ownm.diag.for REGE.nm.for
> ###   REGE.nm.diag.for REGE.ne.for REGE.ow.ne.for REGE.ownm.ne.for
> ###   REGE.nm.ne.for REGD.ne.for REGD.ow.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward.D"),
+    k = 2))
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address 6383f964, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   2.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.5Mb
Running ‘test-all.R’ [36s/87s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("broom.mixed")
  Loading required package: broom.mixed
  
   *** caught segfault ***
  address 0, cause 'memory not mapped'
  
   *** caught segfault ***
  address 4, cause 'memory not mapped'
  Warning: stack imbalance in 'names', 138 then 135
  Warning: stack imbalance in '[[', 138 then 144
  Warning: stack imbalance in '[[<-', 152 then 156
  Warning: stack imbalance in '<-', 136 then 140
  Warning: stack imbalance in 'lazyLoadDBfetch', 147 then 148
  Warning: stack imbalance in '{', 131 then 136
  Warning: stack imbalance in '::', 147 then 149
  Warning: stack imbalance in 'for', 160 then 142
  Warning: stack imbalance in '{', 156 then 138
  Warning: stack imbalance in '
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> ### Name: glance.Rchoice
> ### Title: Glance at a(n) Rchoice object
> ### Aliases: glance.Rchoice
> 
> ### ** Examples
> 
> library(Rchoice)
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
> 
> mod <- Rchoice(vs ~ mpg + hp + factor(cyl),
+                data = mtcars,
+                family = binomial("probit"))
> tidy(mod)
# A tibble: 5 × 5
  term         estimate std.error statistic p.value
  <chr>           <dbl>     <dbl>     <dbl>   <dbl>
1 constant       6.01      4.64     1.30      0.195
2 mpg           -0.0957    0.134   -0.716     0.474
3 hp            -0.0244    0.0214  -1.14      0.253
4 factor(cyl)6  -0.980     1.23    -0.797     0.426
5 factor(cyl)8  -6.39    938.      -0.00682   0.995
> glance(mod)
Error: 'getSummary.Rchoice' is not an exported object from 'namespace:Rchoice'
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   7.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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


Attaching package: 'c3'

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

    grid, legend

Quitting from lines 53-62 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc        4.2Mb
    pictures   3.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           1.0Mb
    htmlwidgets   3.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    extdata   1.6Mb
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘catmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 111-117 (catmaply.Rmd) 
Error: processing vignette 'catmaply.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘catmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [56s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CausalGPS)
  > 
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("CausalGPS")
  2021-07-23 14:13:19 swift-9.stats.ox.ac.uk 16108 CausalGPS log_system_info INFO:  System name: SunOS, OS type: unix, machine architecture: i86pc, user: ripley, R version 4.1.0 Patched (2021-07-20 r80649), detected cores: 16
  2021-07-23 14:13:42 swift-9.stats.ox.ac.uk 16108 CausalGPS compile_pseudo_pop INFO:  Starting compiling pseudo population  (original data size: 100) ... 
  starting worker pid=16716 on localhost:11639 at 14:13:43.418
  2021-07-23 14:13:48 swift-9.stats.ox.ac.uk 16716 CausalGPS FUN WARN:  There is no data to match with  18.9451694492605 in  0.5  radius.
  2021-07-23 14:13:48 swift-9.stats.ox.ac.uk 16716 CausalGPS FUN WARN:  There is no data to match with  20.9451694492605 in  0.5  radius.
  2021-07-23 14:13:48 swift-9.stats.ox.ac.uk 16716 CausalGPS FUN WARN:  There is no data to match with  21.9451694492605 in  0.5  radius.
  2021-07-23 14:13:48 swift-9.stats.ox.ac.uk 16716 CausalGPS FUN WARN:  There is no data to match with  23.9451694492605 in  0.5  radius.
  2021-07-23 14:13:48 swift-9.stats.ox.ac.uk 16108 CausalGPS compile_pseudo_pop INFO:  Finished compiling pseudo population  (Pseudo population data size: 2200)
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-matching_l1.R:30:4): matching_l1 functions as expected. ───────
  val$cf1[10] not equal to -0.8642621.
  1/1 mismatches
  [1] -0.137 - -0.864 == 0.727
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Running examples in ‘CEDARS-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_project
> ### Title: Create a New CEDARS Project
> ### Aliases: create_project
> 
> ### ** Examples
> 
> # The code below creates an instance of CEDARS project on a public test MongoDB cluster, populated
> # with fictitious EHR corpora.
> 
> # MongoDB credentials
> db_user_name <- "testUser"
> db_user_pw <- "testPW"
> db_host <- "cedars.yvjp6.mongodb.net"
> db_port <- NA
> 
> # Using standard MongoDB URL format
> uri_fun <- mongo_uri_standard
> 
> # Name for MongoDB database which will contain the CEDARS project
> # In this case we generate a random name
> mongo_database <- find_project_name()
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-00.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cedars-shard-00-01.yvjp6.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify faile
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.3Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    include  35.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.9Mb
Package suggested but not available for checking: ‘iptools’
Running ‘test-all.R’ [28s/36s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("checkmate")
  Loading required package: checkmate
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_checkNames.R:34:3): checkNames ────────────────────────────────
  testNames("ä", type = "strict") is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  ── Failure (test_checkNames.R:35:3): checkNames ────────────────────────────────
  testNames("ä", type = "ids") is not FALSE
  
  `actual`:   TRUE 
  `expected`: FALSE
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 2899 ]
  Error: Test failures
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chromoMap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 215-217 (chromoMap.Rmd) 
Error: processing vignette 'chromoMap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘chromoMap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chronicle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: magrittr
Quitting from lines 38-67 (chronicle.Rmd) 
Error: processing vignette 'chronicle.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building ‘chronicle.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.6Mb
    help   1.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        6.0Mb
    skeleton   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘clinDataReview-dataPreprocessing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Data annotated with variable(s): ETHNIC ('ETHNIC'), ARM ('ARM') from the 'custom' dataset based on the variable(s):	USUBJID ('USUBJID').
354 records with ARM ('ARM') %in% 'Placebo' are filtered in data.
--- finished re-building ‘clinDataReview-dataPreprocessing.Rmd’

--- re-building ‘clinDataReview-dataVisualization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning: Ignoring unknown aesthetics: text
Quitting from lines 154-187 (clinDataReview-dataVisualization.Rmd) 
Error: processing vignette 'clinDataReview-dataVisualization.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘clinDataReview-dataVisualization.Rmd’

--- re-building ‘clinDataReview-reporting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘clinDataReview-reporting.Rmd’

SUMMARY: processing the following file failed:
  ‘clinDataReview-dataVisualization.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clustcurv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 108-109 (clustcurv.Rmd) 
Error: processing vignette 'clustcurv.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘clustcurv.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 403-416 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       3.5Mb
    extdata   1.8Mb
Running ‘testthat.R’ [9s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(codemetar)
  > 
  > skip_if_offline <- function() skip_if_not(pingr::is_online())
  > test_check("codemetar")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (27)
  • nzchar(Sys.getenv("GITHUB_PAT")) is not TRUE (2)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-codemeta_description.R:62:3): Helper functions work correctly ───
  Error: Timeout was reached: [sysreqs.r-hub.io] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Backtrace:
       █
    1. └─codemetar:::add_software_terms(codemeta, descr) test-codemeta_description.R:62:2
    2.   └─codemetar:::parse_sys_reqs(...)
    3.     └─codemetar:::get_sys_links(pkg, description = sys_reqs, verbose)
    4.       ├─codemetar:::get_url_rhub(...)
    5.       │ └─base::sprintf("https://sysreqs.r-hub.io/%s/%s", a, b)
    6.       ├─base::unique(...)
    7.       └─codemetar:::get_rhub_json_names("pkg", pkg)
    8.         ├─base::sapply(...)
    9.         │ └─base::lapply(X = X, FUN = FUN, ...)
   10.         └─jsonlite::fromJSON(get_url_rhub(a, b), simplifyVector = FALSE)
   11.           └─jsonlite:::parse_and_simplify(...)
   12.             └─jsonlite:::parseJSON(txt, bigint_as_char)
   13.               └─jsonlite:::parse_con(txt, bigint_as_char)
   14.                 ├─base::open(con, "rb")
   15.                 └─base::open.connection(con, "rb")
  
  [ FAIL 1 | WARN 0 | SKIP 29 | PASS 80 ]
  Deleting unused snapshots:
  * _snaps/write_codemeta/codemeta.json
  Error: Test failures
  Execution halted
Found the following files/directories:
  ‘fda7wnr6u.c’
Package suggested but not available for checking: ‘gifski’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘colourvision-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 622-623 (colourvision-vignette.Rmd) 
Error: processing vignette 'colourvision-vignette.Rmd' failed with diagnostics:
length(code) == 1 is not TRUE
--- failed re-building ‘colourvision-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    help   1.4Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RcppArmadillo’ ‘base’ ‘lwgeom’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help          1.0Mb
    htmlwidgets   3.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc             2.3Mb
    vignette_data   2.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   6.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs          2.6Mb
    sample_data   2.8Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(coro)
  > 
  > test_check("coro")
  
  
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘covid19dbcand.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (covid19dbcand.Rmd) 
Error: processing vignette 'covid19dbcand.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘covid19dbcand.Rmd’

SUMMARY: processing the following file failed:
  ‘covid19dbcand.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Package suggested but not available for checking: ‘BSgenome.Scerevisiae.UCSC.sacCer2’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘CPMandPERT.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 104-106 (CPMandPERT.Rmd) 
Error: processing vignette 'CPMandPERT.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘CPMandPERT.Rmd’

--- re-building ‘LESS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-64 (LESS.Rmd) 
Error: processing vignette 'LESS.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LESS.Rmd’

SUMMARY: processing the following files failed:
  ‘CPMandPERT.Rmd’ ‘LESS.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [5s/15s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("crminer")
  Loading required package: crminer
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (15)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-crm_links.R:55:3): crm_links: elife special handling ────────────
  Error: res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
  Backtrace:
      █
   1. └─crminer::crm_links("10.7554/elife.04059") test-crm_links.R:55:2
   2.   └─crminer:::crm_works_links(dois = doi, ...)
   3.     ├─stats::setNames(lapply(dois, get_links, ...), dois)
   4.     └─base::lapply(dois, get_links, ...)
   5.       └─crminer:::FUN(X[[i]], ...)
   6.         └─crminer:::crm_GET(sprintf("works/%s", x), NULL, FALSE, ...)
   7.           └─base::stopifnot(res$response_headers$`content-type` == "application/json;charset=UTF-8")
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 80 ]
  Error: Test failures
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘future’
  All declared Imports should be used.
Running examples in ‘ctsemOMX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctGenerateFromFit
> ### Title: Generates data according to the model estimated in a ctsemFit
> ###   object.
> ### Aliases: ctGenerateFromFit
> 
> ### ** Examples
> 
> 
> data(AnomAuth) 
> AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2), 
+   Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2)) 
Type "omx" is still supported but requires ctsemOMX package installation. "stanct" or "standt" are recommended types.
> AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
wide format data detected
Running ctsemCarefulFit with 14 parameters
Running ctsem with 14 parameters

Beginning initial fit attempt
Running ctsem with 14 parameters
terminate called after throwing an instance of 'std::runtime_error'
  what():  std::bad_alloc
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.8Mb
    doc    1.1Mb
    libs   5.5Mb
Packages which this enhances but not available for checking:
  'Rcplex', 'gurobi', 'rcbc', 'Rmosek'
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Variable(3,3, PSD = TRUE))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: scs::scs(A = args$A, b = args$b, obj = args$c, cone = cones,     control = control)
 2: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 3: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 4: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 5: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 6: psolve(a, solver = NA, ...)
 7: psolve(a, solver = NA, ...)
 8: solve(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    img   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-74 (DA.Rmd) 
Error: processing vignette 'DA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘DA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    deps  11.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    lib   8.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    deps   7.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       2.4Mb
    extdata   1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
File ‘dcortools/libs/dcortools.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Objects: ‘RcppExports.o’, ‘matrix_vector_operations.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Package suggested but not available for checking: ‘XLConnect’
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   2.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.0Mb
    help   1.6Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-56 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
there is no package called 'Rcpp'
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    doc           9.9Mb
    htmlwidgets   3.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    help   1.3Mb
Package suggested but not available for checking: ‘plumberDeploy’
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    include  14.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
Found the following files/directories:
  ‘RtmpI_aWyq’ ‘RtmpnCaq_y’
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    assets   3.4Mb
    doc      2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   3.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    appinformation   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 56-57 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    1.9Mb
    help   2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DSjobtracker.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'magrittr'

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

    extract


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

Loading required package: viridisLite
Selecting by Total
Quitting from lines 136-155 (DSjobtracker.Rmd) 
Error: processing vignette 'DSjobtracker.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘DSjobtracker.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 164-165 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dub-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: DUBStepR
Attaching SeuratObject

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

Quitting from lines 63-65 (dub-vignette.Rmd) 
Error: processing vignette 'dub-vignette.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘dub-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.2Mb
Running ‘testthat.R’ [515s/152s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  ❌ Unable to read hdf5 files
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-h5.R:11:3): write_h5 and read_h5 works ──────────────────────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. └─dynutils::read_h5(file) test-h5.R:11:2
   2.   └─dynutils::read_h5_(file_h5)
   3.     └─hdf5r::h5attr(file_h5, "object_class")
   4.       └─attr_obj$read()
   5.         └─hdf5r:::H5ToR_Pre(mem_type, nelem)
  ── Error (test-h5.R:17:3): test_h5_installation works ──────────────────────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. ├─testthat::expect_true(test_h5_installation()) test-h5.R:17:2
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─dynutils::test_h5_installation()
   5.   └─dynutils:::test_h5_installation_read(detailed, file)
   6.     └─base::tryCatch(...)
   7.       └─base:::tryCatchList(expr, classes, parentenv, handlers)
   8.         └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9.           └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 546 ]
  Error: Test failures
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘gurobi’
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc       6.2Mb
    extdata   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 325-330 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    xsd   4.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
--- finished re-building ‘epicontacts_class.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   8.5Mb
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
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: ‘mzR’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    2.3Mb
    libs   1.0Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc  13.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    shiny     2.1Mb
Package suggested but not available for checking: ‘corehunter’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Running examples in ‘ExhaustiveSearch-Ex.R’ failed
The error most likely occurred in:

> ### Name: ExhaustiveSearch
> ### Title: Exhaustive feature selection
> ### Aliases: ExhaustiveSearch
> 
> ### ** Examples
> 
> ## Linear Regression on mtcars data
> data(mtcars)
> 
> ##  Exhaustive search of 1023 models compared by AIC
> ES <- ExhaustiveSearch(mpg ~ ., data = mtcars, family = "gaussian",
+   performanceMeasure = "AIC")

Starting the exhaustive evaluation.

 Runtime          |  Completed  |  Status
------------------------------------------

 *** caught segfault ***
address 6666666e, cause 'memory not mapped'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    exiftool  15.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-faq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (Intro-faq.Rmd) 
Error: processing vignette 'Intro-faq.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro-faq.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-faq.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.8Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    help   1.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘seasonal’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data-Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dm'

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

    filter

Quitting from lines 36-39 (Data-Model.Rmd) 
Error: processing vignette 'Data-Model.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Data-Model.Rmd’

--- re-building ‘fishdata-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

`summarise()` has grouped output by 'site'. You can override using the `.groups` argument.
--- finished re-building ‘fishdata-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘Data-Model.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_fishflux.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 81-123 (intro_to_fishflux.Rmd) 
Error: processing vignette 'intro_to_fishflux.Rmd' failed with diagnostics:
Please install either RStudio or Pandoc (https://pandoc.org)
--- failed re-building ‘intro_to_fishflux.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   4.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbit_viz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-173 (fitbit_viz.Rmd) 
Error: processing vignette 'fitbit_viz.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘fitbit_viz.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro-flashCard.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 26-32 (Intro-flashCard.Rmd) 
Error: processing vignette 'Intro-flashCard.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro-flashCard.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro-flashCard.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘multipanelfigure’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R   7.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony', 'mvoutlier'
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   2.2Mb
    libs   6.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/home/ripley/R/packages/tests32/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   5.0Mb
    doc    1.7Mb
    help   1.5Mb
    libs   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘fRLR.Rnw’ using Sweave
Warning: stack imbalance in 'withVisible', 33 then 42
Packages suggested but not available for checking: 'foba', 'rrlda', 'RWeka'
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > # required packages
  > library(testthat)
  > library(fst)
  > 
  > # some helper functions
  > source("testthat/helper_fstwrite.R")  # cross-version testing
  > 
  > # run tests
  > test_check("fst")
  
   *** caught segfault ***
  address 50564a3f, cause 'memory not mapped'
installed size is  5.6Mb
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    extdata   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘GALLO.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 45-59 (GALLO.Rmd) 
Error: processing vignette 'GALLO.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘GALLO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc  44.5Mb
installed size is  7.0Mb
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    doc   6.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- 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:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.1Mb
    libs     2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.4Mb
Package suggested but not available for checking: ‘mlpack’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   5.5Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    R         9.1Mb
    extdata   1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geometr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 268-300 (geometr.Rmd) 
Error: processing vignette 'geometr.Rmd' failed with diagnostics:
Problem with `mutate()` column `deciduous`.
ℹ `deciduous = c(T, T, F, F, F, T, T, F, T, T, F)`.
ℹ `deciduous` must be size 0 or 1, not 11.
--- failed re-building ‘geometr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using formula 'y ~ x'
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    help       2.2Mb
    testdata   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fully-customed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘fully-customed.Rmd’

--- re-building ‘using-ggVennDiagram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 73-81 (using-ggVennDiagram.Rmd) 
Error: processing vignette 'using-ggVennDiagram.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘using-ggVennDiagram.Rmd’

--- re-building ‘using-new-shapes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using-new-shapes.Rmd’

--- re-building ‘venn-plot-with-more-than-four-sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘venn-plot-with-more-than-four-sets.Rmd’

SUMMARY: processing the following file failed:
  ‘using-ggVennDiagram.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs            1.9Mb
    test_data       2.2Mb
    vignette_data   1.3Mb
Running examples in ‘glmmTMB-Ex.R’ failed
The error most likely occurred in:

> ### Name: VarCorr.glmmTMB
> ### Title: Extract variance and correlation components
> ### Aliases: VarCorr.glmmTMB VarCorr
> ### Keywords: internal
> 
> ### ** Examples
> 
> ## Comparing variance-covariance matrix with manual computation
> data("sleepstudy",package="lme4")
> fm4 <- glmmTMB(Reaction ~ Days + (Days|Subject), sleepstudy)

 *** caught segfault ***
address 0, cause 'memory not mapped'

 *** caught segfault ***
address bf668c08, cause 'memory not mapped'

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
An irrecoverable exception occurred. R is aborting now ...

Traceback:
 1: retape(set.defaults = TRUE)
 2: MakeADFun(data.tmb, parameters, map = mapArg, random = randomArg,     profile = NULL, silent = !verbose, DLL = "glmmTMB")
 3: eval(substitute(expr), data, enclos = parent.frame())
 4: eval(substitute(expr), data, enclos = parent.frame())
 5: with.default(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 6: with(TMBStruc, MakeADFun(data.tmb, parameters, map = mapArg,     random = randomArg, profile = NULL, silent = !verbose, DLL = "glmmTMB"))
 7: fitTMB(TMBStruc)
 8: glmmTMB(Reaction ~ Days + (Days | Subject), sleepstudy)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: cox.path
> ### Title: Fit a Cox regression model with elastic net regularization for a
> ###   path of lambda values
> ### Aliases: cox.path
> 
> ### ** Examples
> 
> set.seed(2)
> nobs <- 100; nvars <- 15
> xvec <- rnorm(nobs * nvars)
> xvec[sample.int(nobs * nvars, size = 0.4 * nobs * nvars)] <- 0
> x <- matrix(xvec, nrow = nobs)
> beta <- rnorm(nvars / 3)
> fx <- x[, seq(nvars / 3)] %*% beta / 3
> ty <- rexp(nobs, exp(fx))
> tcens <- rbinom(n = nobs, prob = 0.3, size = 1)
> jsurv <- survival::Surv(ty, tcens)
> fit1 <- glmnet:::cox.path(x, jsurv)
> 
> # works with sparse x matrix
> x_sparse <- Matrix::Matrix(x, sparse = TRUE)
> fit2 <- glmnet:::cox.path(x_sparse, jsurv)
Error in elnet.fit(x, z, w, lambda, alpha, intercept = FALSE, thresh = thresh,  : 
  NA/NaN/Inf in foreign function call (arg 23)
Calls: <Anonymous> -> cox.fit -> elnet.fit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Coxnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

(process:18845): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9'

(process:18845): Pango-WARNING **: font_face status is: <unknown error status>

(process:18845): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:18845): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9', text='m'
Quitting from lines 191-193 (Coxnet.Rmd) 
Error: processing vignette 'Coxnet.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 19)
--- failed re-building ‘Coxnet.Rmd’

--- re-building ‘glmnet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loaded lars 1.2

--- finished re-building ‘glmnet.Rmd’

--- re-building ‘glmnetFamily.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 4.1-2
Quitting from lines 86-89 (glmnetFamily.Rmd) 
Error: processing vignette 'glmnetFamily.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 25)
--- failed re-building ‘glmnetFamily.Rmd’

--- re-building ‘relax.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘relax.Rmd’

SUMMARY: processing the following files failed:
  ‘Coxnet.Rmd’ ‘glmnetFamily.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running ‘testthat.R’ [21s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GpGp)
  > 
  > test_check("GpGp")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_loglik.R:33:5): likelihood approximations are exact when m = n-1 ──
  llobj$loglik not equal to `ll_exact`.
  1/1 mismatches
  [1] 217 - 62.7 == 155
  ── Failure (test_loglik.R:39:5): likelihood approximations are exact when m = n-1 ──
  llobj$loglik not equal to `ll_exact`.
  1/1 mismatches
  [1] 217 - 62.7 == 155
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 117 ]
  Error: Test failures
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 243-244 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   4.5Mb
Packages required but not available: 'seasonal', 'x13binary'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.6Mb
installed size is 169.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    java  166.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    HaDeX   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘staplr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘haplor-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
URL does not seem to exist: https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php
Here's the original error message:
XML content does not seem to be XML: ''
Quitting from lines 279-288 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
object 'out' not found
--- failed re-building ‘haplor-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   1.1Mb
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
> h5attr(file, "attr_numeric") <- rnorm(10)
> a <- file$attr_open("attr_numeric")
> a$get_info()
  corder_valid corder cset data_size
1            0      0    0        80
> a$attr_name()
[1] "attr_numeric"
> a$get_space()
Class: H5S
Type: Simple
Dims: 10
Maxdims: 10
> a$get_type()
Class: H5T_FLOAT
Datatype: H5T_IEEE_F64LE
> a$get_storage_size()
[1] 80
> a$read()
Error in H5ToR_Pre(mem_type, nelem) : HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: <Anonymous> -> H5ToR_Pre
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 159-160 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

(process:28203): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:28203): Pango-WARNING **: font_face status is: no error has occurred

(process:28203): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:28203): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 87-94 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘kmeans-umap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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: The `x` argument of `as_tibble.matrix()` must have unique column names if `.name_repair` is omitted as of tibble 2.0.0.
Using compatibility `.name_repair`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Joining, by = "service_line"
--- finished re-building ‘kmeans-umap.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.2.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Quitting from lines 109-111 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hermiter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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


Attaching package: 'data.table'

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

    between, first, last

Quitting from lines 542-544 (hermiter.Rmd) 
Error: processing vignette 'hermiter.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hermiter.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests32/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package suggested but not available for checking: ‘trackr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   4.5Mb
    doc    1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   6.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hyperoverlap-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 51-58 (hyperoverlap-vignette.Rmd) 
Error: processing vignette 'hyperoverlap-vignette.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘hyperoverlap-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_iBreakDown_description.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.1).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
--- finished re-building ‘vignette_iBreakDown_description.Rmd’

--- re-building ‘vignette_iBreakDown_titanic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.1).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?
Quitting from lines 91-92 (vignette_iBreakDown_titanic.Rmd) 
Error: processing vignette 'vignette_iBreakDown_titanic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vignette_iBreakDown_titanic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.1000genomes.hs37d5’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

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

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address a61a78f8, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    dlib-19.20   8.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       4.4Mb
    extdata   1.2Mb
    include   3.0Mb
    libs      6.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
    doc    1.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.3Mb
Package unavailable to check Rd xrefs: ‘minfi’
Running ‘testthat.R’ [32m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DALEX)
  Welcome to DALEX (version: 2.2.1).
  Find examples and detailed introduction at: http://ema.drwhy.ai/
  Additional features will be available after installation of: ggpubr.
  Use 'install_dependencies()' to get all suggested dependencies
  > library(ingredients)
  
  Attaching package: 'ingredients'
  
  The following object is masked from 'package:DALEX':
  
      feature_importance
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("ingredients")
  Aggregating predictions.. Progress: 90%. Estimated remaining time: 3 seconds.
  Aggregating predictions.. Progress: 79%. Estimated remaining time: 8 seconds.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Package suggested but not available for checking: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R  11.8Mb
Package suggested but not available for checking: ‘xcms’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    app    4.3Mb
    data   1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘general-introduction-to-justifier.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘general-introduction-to-justifier.Rmd’

--- re-building ‘justifier-in-intervention-development.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘justifier-in-intervention-development.Rmd’

--- re-building ‘justifier-in-study-design.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 268-269 (justifier-in-study-design.Rmd) 
Error: processing vignette 'justifier-in-study-design.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘justifier-in-study-design.Rmd’

SUMMARY: processing the following file failed:
  ‘justifier-in-study-design.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘awesome_table_in_html.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 635-638 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘awesome_table_in_html.Rmd’

--- re-building ‘awesome_table_in_pdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘awesome_table_in_pdf.Rmd’

--- re-building ‘best_practice_for_newline_in_latex_table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘best_practice_for_newline_in_latex_table.Rmd’

--- re-building ‘legacy_features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘legacy_features.Rmd’

--- re-building ‘use_kable_in_shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘use_kable_in_shiny.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/kdtools.Rcheck/00install.out’ for details.
File ‘KernelICA/libs/KernelICA.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Objects: ‘KernelICAProblem.o’, ‘RcppExports.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘kgc-fine.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
--- failed re-building ‘kgc-fine.Rmd’

--- re-building ‘kgc-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
--- finished re-building ‘kgc-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kgc-fine.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   1.4Mb
Package suggested but not available for checking: ‘Rmosek’
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘SnowballC’ ‘stringi’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gpg’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data             1.0Mb
    doc              1.0Mb
    shiny-landsepi   1.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.0Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.2Mb
    libs   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘LDATS_codebase.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘LDATS_codebase.Rmd’

--- re-building ‘paper-comparison.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (paper-comparison.Rmd) 
Error: processing vignette 'paper-comparison.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘paper-comparison.Rmd’

--- re-building ‘rodents-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘rodents-example.Rmd’

SUMMARY: processing the following file failed:
  ‘paper-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘RtmpA_aq1h’
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage-leaflet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sp
Quitting from lines 32-38 (usage-leaflet.Rmd) 
Error: processing vignette 'usage-leaflet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘usage-leaflet.Rmd’

--- re-building ‘usage-leafletProxy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘usage-leafletProxy.Rmd’

SUMMARY: processing the following file failed:
  ‘usage-leaflet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   4.8Mb
Namespaces in Imports field not imported from:
  ‘cli’ ‘glue’ ‘stringr’
  All declared Imports should be used.
Compilation used the following non-portable flag(s):
  ‘-mt’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    2.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘linkspotterVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.4Mb
    testdata   1.4Mb
Package suggested but not available for checking: ‘Rsymphony’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

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

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

> ### Name: StEM_mirt
> ### Title: Stochastic EM algorithm for solving multivariate item response
> ###   theory model
> ### Aliases: StEM_mirt
> 
> ### ** Examples
> 
> # run a toy example based on the M2PL model
> 
> # load a simulated dataset
> attach(data_sim_mirt)
> 
> # generate starting values for the algorithm
> A0 <- Q
> d0 <- rep(0, J)
> theta0 <- matrix(rnorm(N*K, 0, 1),N)
> sigma0 <- diag(1, K) 
> 
> # do the confirmatory MIRT analysis
> # to enable multicore processing, set parallel = T
> mirt_res <- StEM_mirt(response, Q, A0, d0, theta0, sigma0)

Step  1	| 
Step  2	| 
Step  3	| 
Step  4	|
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-9
lavaan is FREE software! Please report any bugs.
> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: C stack usage  330994836 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  'av', 'rsvg', 'tesseract', 'gifski'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 227-236 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
R: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4372
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘latin_square.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-91 (latin_square.Rmd) 
Error: processing vignette 'latin_square.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘latin_square.Rmd’

--- re-building ‘make_prior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-145 (make_prior.Rmd) 
Error: processing vignette 'make_prior.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘make_prior.Rmd’

--- re-building ‘neonatal_mortality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘neonatal_mortality.Rmd’

--- re-building ‘wheat_breeding.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 94-95 (wheat_breeding.Rmd) 
Error: processing vignette 'wheat_breeding.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wheat_breeding.Rmd’

SUMMARY: processing the following files failed:
  ‘latin_square.Rmd’ ‘make_prior.Rmd’ ‘wheat_breeding.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘manipulateWidgets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.2Mb
    help   1.6Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data          1.4Mb
    doc           1.6Mb
    htmlwidgets   2.3Mb
    libs          2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    data   2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 114-119 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Packages suggested but not available for checking: 'REBayes', 'flashr'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in ‘mcboost-Ex.R’ failed
The error most likely occurred in:

> ### Name: MCBoost
> ### Title: Multi-Calibration Boosting
> ### Aliases: MCBoost
> 
> ### ** Examples
> 
>   # See vignette for more examples.
>   # Instantiate the object
>   mc = MCBoost$new()
>   # Run multi-calibration on training dataset.
>   mc$multicalibrate(iris[1:100,1:4], factor(sample(c("A","B"), 100, TRUE)))
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: <Anonymous> ... NextMethod -> predict.glmnet -> lambda.interp -> approx
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Running examples in ‘mdendro-Ex.R’ failed
The error most likely occurred in:

> ### Name: linkage
> ### Title: Extended Agglomerative Hierarchical Clustering
> ### Aliases: linkage descplot
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## Plot and summary of unweighted arithmetic linkage (UPGMA) dendrogram
> lnk1 <- linkage(UScitiesD)
> plot(lnk1)
> summary(lnk1)
linkage(prox = UScitiesD,
        type.prox = "distance",
        digits = 0,
        method = "arithmetic",
        weighted = FALSE,
        group = "variable")

      cor       sdr        ac        cc        tb 
0.8101937 0.6998814 0.7059747 0.3055556 0.9316262 
> 
> ## Linkage of similarity data (non-negative correlations)
> sim <- as.dist(cor(EuStockMarkets))
> lnk2 <- linkage(sim, type.prox = "similarity")
Error in rcppLinkage(prox = prox, isDistance = (type.prox == "distance"),  : 
  std::bad_alloc
Calls: linkage -> rcppLinkage
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mdendro-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-104 (mdendro-vignette.Rmd) 
Error: processing vignette 'mdendro-vignette.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘mdendro-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MedLEA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
✔ ggplot2 3.3.5     ✔ purrr   0.3.4
✔ tibble  3.1.2     ✔ dplyr   1.0.7
✔ tidyr   1.1.3     ✔ stringr 1.4.0
✔ readr   2.0.0     ✔ forcats 0.5.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Loading required package: NLP

Attaching package: 'NLP'

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

    annotate

Warning in tm_map.SimpleCorpus(., stripWhitespace) :
  transformation drops documents
Quitting from lines 23-39 (MedLEA.Rmd) 
Error: processing vignette 'MedLEA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘MedLEA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    help   1.8Mb
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'No predictor' exited abnormally with the error message: User interrupt>
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt>
Warning: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt
        Length Class  Mode     
message 1      -none- character
call    0      -none- NULL     
> 
> ## Multivariate meta-analysis on the log of the odds
> ## The conditional sampling covariance is 0
> bcg <- meta(y=cbind(ln_Odd_V, ln_Odd_NV), data=BCG,
+             v=cbind(v_ln_Odd_V, cov_V_NV, v_ln_Odd_NV))
Error: C stack usage  279483540 is too close to the limit
Error in running mxModel:
<simpleError: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt>
Warning: The job for model 'Meta analysis with ML' exited abnormally with the error message: User interrupt
> summary(bcg)
        Length Class  Mode     
message 1      -none- character
call    0      -none- NULL     
> 
> plot(bcg)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.0Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    5.7Mb
    libs   1.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgcviz.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-36. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

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

    qqline, qqnorm, qqplot

Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 173-181 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘mgcviz.rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
--- failed re-building ‘Analysis.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:3941): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:3941): Pango-WARNING **: font_face status is: <unknown error status>

(process:3941): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:3941): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9.9599609375', text='m'
Loading required package: Matrix
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Level2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
--- finished re-building ‘Level2.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Installation failed.
See ‘/home/ripley/R/packages/tests32/mlpack.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking:
  'FSelector', 'rrlda', 'RWeka'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    images   1.4Mb
    shiny   15.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: dfidx

Attaching package: 'dfidx'

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

    filter


Attaching package: 'mlogit'

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

    hmftest, index, scoretest

Loading required package: stats4
Loading required package: splines

Attaching package: 'VGAM'

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

    has.intercept, lrtest

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

    lrtest
Running ‘spelling.R’
  Running ‘testthat.R’ [418s/263s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelbased)
  > 
  > osx <- tryCatch(
  +   {
  +     si <- Sys.info()
  +     if (!is.null(si["sysname"])) {
  +       si["sysname"] == "Darwin" || grepl("^darwin", R.version$os)
  +     } else {
  +       FALSE
  +     }
  +   },
  +   error = function(e) {
  +     FALSE
  +   }
  + )
  > 
  > if (!osx || (osx && getRversion() >= "4.0.0")) {
  +   test_check("modelbased")
  + }
  Starting 2 test processes
  
  
  Error: testthat subprocess exited in file `test-estimate_predicted.R`
  Backtrace:
       █
    1. └─testthat::test_check("modelbased")
    2.   └─testthat::test_dir(...)
    3.     └─testthat:::test_files(...)
    4.       └─testthat:::test_files(...)
    5.         ├─testthat::with_reporter(...)
    6.         │ ├─base::withRestarts(...)
    7.         │ │ └─base:::withOneRestart(expr, restarts[[1L]])
    8.         │ │   └─base:::doWithOneRestart(return(expr), restart)
    9.         │ └─base::force(code)
   10.         └─testthat:::parallel_event_loop_chunky(queue, reporters)
   11.           └─queue$poll(Inf)
   12.             └─base::lapply(...)
   13.               └─testthat:::FUN(X[[i]], ...)
   14.                 └─private$handle_error(msg, i)
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ms-perks-features.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-perks-features.Rmd’

--- re-building ‘ms-r-python-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ms-r-python-examples.Rmd’

--- re-building ‘ms-rmarkdown.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Welcome to DALEX (version: 2.2.1).
Find examples and detailed introduction at: http://ema.drwhy.ai/
Additional features will be available after installation of: ggpubr.
Use 'install_dependencies()' to get all suggested dependencies
`new_observation` argument is NULL. `new_observation_n` observations needed to calculate local explanations are taken from the data.

Quitting from lines 59-75 (ms-rmarkdown.Rmd) 
Error: processing vignette 'ms-rmarkdown.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ms-rmarkdown.Rmd’

SUMMARY: processing the following file failed:
  ‘ms-rmarkdown.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc  23.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘molaR_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 58-60 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘molaR_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets  15.3Mb
Running examples in ‘mongolite-Ex.R’ failed
The error most likely occurred in:

> ### Name: gridfs
> ### Title: GridFS API
> ### Aliases: gridfs
> 
> ### ** Examples
> 
> # Upload a file to GridFS
> fs <- gridfs(url = "mongodb+srv://readwrite:test@cluster0-84vdt.mongodb.net/test")
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-01-84vdt.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-02-84vdt.mongodb.net:27017'] [TLS handshake failed: error:14090086:SSL routines:ssl3_get_server_certificate:certificate verify f
Execution halted
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsageOfMrSGUIDE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-120 (UsageOfMrSGUIDE.Rmd) 
Error: processing vignette 'UsageOfMrSGUIDE.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘UsageOfMrSGUIDE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-103 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    www   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘leukemiasEset’
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc    6.6Mb
    libs   6.8Mb
Running examples in ‘mxmmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxMmodModel
> ### Title: Create an MMOD
> ### Aliases: mxMmodModel
> 
> ### ** Examples
> 
> data(nlsy97depression)
> # Fit one factor MMOD
> structure <- list(
+   F1 = c('nervous', 'down', 'depressed', 'calm', 'happy')
+ )
> mmod_model <- mxMmodModel(data=nlsy97depression,
+                           modelName='1 Factor MMOD',
+                           idvar='pid', timevar='occasion', structure=structure)
Warning in mxMmodModel(data = nlsy97depression, modelName = "1 Factor MMOD",  :
  Missing values detected; omitting them.
> mmod_fit <- OpenMx::mxRun(mmod_model)
Running 1 Factor MMOD with 33 parameters

 *** caught segfault ***
address 4938c8a8, cause 'memory not mapped'

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer,     beginMessage)
 2: OpenMx::mxRun(mmod_model)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [10s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mxmmod)
  > 
  > test_check("mxmmod")
  terminate called after throwing an instance of 'std::runtime_error'
    what():  std::bad_array_new_length
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
Running examples in ‘NADIA-Ex.R’ failed
The error most likely occurred in:

> ### Name: PipeOpSample_B
> ### Title: PipeOpSample_B
> ### Aliases: PipeOpSample_B
> 
> ### ** Examples
> 
> {
+   graph <- PipeOpSample_B$new() %>>% mlr3learners::LearnerClassifGlmnet$new()
+   graph_learner <- GraphLearner$new(graph)
+ 
+   # Task with NA
+   set.seed(1)
+   resample(tsk("pima"), graph_learner, rsmp("cv", folds = 3))
+ }
INFO  [13:38:59.464] [mlr3]  Applying learner 'impute_sample_B.classif.glmnet' on task 'pima' (iter 2/3) 
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: resample ... resolve.list -> signalConditionsASAP -> signalConditions
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Errors_Statistic_and_Handling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Errors_Statistic_and_Handling.Rmd’

--- re-building ‘NADIA_examples_and_motivation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-156 (NADIA_examples_and_motivation.Rmd) 
Error: processing vignette 'NADIA_examples_and_motivation.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘NADIA_examples_and_motivation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data     2.0Mb
    libs     1.9Mb
    models   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Installation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Installation.Rmd’

--- re-building ‘neurons-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: rgl
Registered S3 method overwritten by 'nat':
  method             from
  as.mesh3d.ashape3d rgl 
Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.

Attaching package: 'nat'

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

    intersect, setdiff, union

Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 413-417 (neurons-intro.Rmd) 
Error: processing vignette 'neurons-intro.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘neurons-intro.Rmd’

SUMMARY: processing the following file failed:
  ‘neurons-intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘natstrat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 71-81 (natstrat.Rmd) 
Error: processing vignette 'natstrat.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘natstrat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.7-0 (2021-06-25) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/NestedCategBayesImpute.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NetRep)
  > 
  > test_check("NetRep")
  
   *** caught segfault ***
  address eeb4e379, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

 *** caught segfault ***
address aa419af7, cause 'memory not mapped'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 74-75 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10000 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_nimbleEcology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 156-160 (Introduction_to_nimbleEcology.Rmd) 
Error: processing vignette 'Introduction_to_nimbleEcology.Rmd' failed with diagnostics:
Failed to create the shared library. Run 'printErrors()' to see the compilation errors.

--- failed re-building ‘Introduction_to_nimbleEcology.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 26.8Mb
  sub-directories of 1Mb or more:
    CppCode  10.9Mb
    R         6.1Mb
    include   5.4Mb
    libs      3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc   7.5Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    examples   7.2Mb
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.03 0.037 0.069
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.0Mb
    doc    2.3Mb
    help   3.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/ondisc.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RMark', 'R2ucare'
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘umx’
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R        2.8Mb
    data     1.0Mb
    libs     4.3Mb
    models   4.5Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error: C stack usage  271815828 is too close to the limit
Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Package suggested but not available for checking: ‘RcppSimdJson’
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         2.1Mb
    shiny-app   1.0Mb
Running ‘exporting-methods.R’
  Running ‘testthat.R’ [55s/66s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 204-226 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    9.4Mb
    libs   3.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PandemicLP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (PandemicLP.Rmd) 
Error: processing vignette 'PandemicLP.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP.Rmd’

--- re-building ‘PandemicLP_SumRegions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

Quitting from lines 172-175 (PandemicLP_SumRegions.Rmd) 
Error: processing vignette 'PandemicLP_SumRegions.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP_SumRegions.Rmd’

SUMMARY: processing the following files failed:
  ‘PandemicLP.Rmd’ ‘PandemicLP_SumRegions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parallelplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-26 (introduction-to-parallelplot.Rmd) 
Error: processing vignette 'introduction-to-parallelplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parallelplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘M3C’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lib   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   8.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc   8.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

`curl` package not installed, falling back to using `url()`
`curl` package not installed, falling back to using `url()`
Quitting from lines 93-133 (pdxTrees-vignette.Rmd) 
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘pdxTrees-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.4Mb
    help   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   1.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.png’
Running examples in ‘PLNmodels-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.PLNmixturefit
> ### Title: Mixture visualization of a 'PLNmixturefit' object
> ### Aliases: plot.PLNmixturefit
> 
> ### ** Examples
> 
> data(trichoptera)
> trichoptera <- prepare_data(trichoptera$Abundance, trichoptera$Covariate)
> myPLN <- PLNmixture(Abundance ~ 1 + offset(log(Offset)),
+            data = trichoptera, control_main = list(iterates = 0))  %>% getBestModel()

 Initialization...

 Adjusting 5 PLN mixture models.
	number of cluster = 1 
	number of cluster = 2 
	number of cluster = 3 
	number of cluster = 4 
	number of cluster = 5 

 Smoothing PLN mixture models.

 Post-treatments
 DONE!
> plot(myPLN, "pca")
> plot(myPLN, "matrix")
Warning: Transformation introduced infinite values in discrete y-axis
Error in seq.default(min, max, by = by) : 'from' must be a finite number
Calls: plot ... <Anonymous> -> f -> <Anonymous> -> seq -> seq.default
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.7Mb
Running ‘spelling.R’
  Running ‘testthat.R’ [1m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plumber)
  > 
  > test_check("plumber")
  
  
  Execution halted
Running ‘testthat.R’ [48s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_invertpmultinom.R:37:3): Correct behavior when target probability is 0 or 1 ──
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 6 - 0 == 6
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1561 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘about-podr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-64 (about-podr.Rmd) 
Error: processing vignette 'about-podr.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘about-podr.Rmd’

SUMMARY: processing the following file failed:
  ‘about-podr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    help   3.0Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      6.6Mb
    data   4.6Mb
    doc    1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    test   1.2Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
Running examples in ‘potential-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_matrix
> ### Title: Create a Distance Matrix Between Two Spatial Objects
> ### Aliases: create_matrix
> 
> ### ** Examples
> 
> g <- create_grid(x = n3_poly, res = 200000)
> mat <- create_matrix(x = n3_pt, y = g)
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: create_matrix ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
Running ‘tinytest.R’ [9s/11s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if (requireNamespace("tinytest", quietly = TRUE)) {
  +   tinytest::test_package("potential")
  + }
  
  test_curv.R...................    0 tests    
  test_curv.R...................    0 tests    
  test_curv.R...................    1 tests [0;32mOK[0m 
  test_curv.R...................    2 tests [0;32mOK[0m 
  test_curv.R...................    3 tests [0;32mOK[0m 
  test_curv.R...................    3 tests [0;32mOK[0m 
  test_curv.R...................    4 tests [0;32mOK[0m 
  test_curv.R...................    5 tests [0;31m1 fails[0m 
  test_curv.R...................    5 tests [0;31m1 fails[0m 
  test_curv.R...................    6 tests [0;31m1 fails[0m Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
    OGRCreateCoordinateTransformation() returned NULL: PROJ available?
  Calls: <Anonymous> ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
  In addition: Warning message:
  In CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
    GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘potential.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0
This project is in maintenance mode. 
Core functionalities of `cartography` can be found in `mapsf`.
https://riatelab.github.io/mapsf/
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Quitting from lines 214-216 (potential.Rmd) 
Error: processing vignette 'potential.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
--- failed re-building ‘potential.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 130-131 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘prettyglm-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 88-90 (prettyglm-vignette.Rmd) 
Error: processing vignette 'prettyglm-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘prettyglm-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'lpsymphony', 'Rsymphony'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    2.3Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in getPrisma(studyStatus) :
  prismaFormat is null so attempting to make automatic one from studyStatus
Warning in getFormatNode(prismaFormat) :
  fontSize param not passed in prismaFormat
Quitting from lines 43-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc           9.0Mb
    htmlwidgets   2.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        4.3Mb
    examples   2.9Mb
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(testthat))
  > suppressPackageStartupMessages(library(pulsar))
  > 
  > testthat::test_check("pulsar")
  
   *** caught segfault ***
  address 33333338, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Example_Save_Data_as_CSV.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Example_Save_Data_as_CSV.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in monitor_dailyStatistic(PacNW, FUN = mean, minHours = 20) :
  Found 2 timezones. Only 'America/Los_Angeles' will be used
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 161-162 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PWFSLSmoke.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   3.4Mb
    libs      2.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

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

> ### Name: corpus-class
> ### Title: Base method extensions for corpus objects
> ### Aliases: corpus-class +.corpus c.corpus [.corpus print.summary.corpus
> ### Keywords: corpus internal
> 
> ### ** Examples
> 
> # concatenate corpus objects
> corp1 <- corpus(data_char_ukimmig2010[1:2])
> corp2 <- corpus(data_char_ukimmig2010[3:4])
> corp3 <- corpus(data_char_ukimmig2010[5:6])
> summary(c(corp1, corp2, corp3))
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'which': Illegal argument. (U_ILLEGAL_ARGUMENT_ERROR, context=`^\p{emoji_presentation}+$`)
Calls: summary ... stri_detect_regex -> .handleSimpleError -> h -> .handleSimpleError -> h
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Package version: 3.0.0
Unicode version: 7.0
ICU version: 55.1
Parallel computing: 16 of 16 threads used.
See https://quanteda.io for tutorials and examples.
Quitting from lines 80-82 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'as.list': error in evaluating the argument 'x' in selecting a method for function 'which': Illegal argument. (U_ILLEGAL_ARGUMENT_ERROR, context=`^\p{emoji_presentation}+$`)
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    java   4.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc  10.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘r3dmol.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-66 (r3dmol.Rmd) 
Error: processing vignette 'r3dmol.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘r3dmol.Rmd’

--- re-building ‘style-functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (style-functions.Rmd) 
Error: processing vignette 'style-functions.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘style-functions.Rmd’

SUMMARY: processing the following files failed:
  ‘r3dmol.Rmd’ ‘style-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘batchelor’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    app   6.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘a01_GettingStarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-78 (a01_GettingStarted.Rmd) 
Error: processing vignette 'a01_GettingStarted.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘a01_GettingStarted.Rmd’

--- re-building ‘a02_VitalRates.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a02_VitalRates.Rmd’

--- re-building ‘a03_LifeHistoryTraits.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a03_LifeHistoryTraits.Rmd’

--- re-building ‘a04_AgeFromStage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a04_AgeFromStage.Rmd’

SUMMARY: processing the following file failed:
  ‘a01_GettingStarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RAhrefs)
  > test_check("RAhrefs")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_auth.R:10:3): api_key param doesn't accept wrong values ───────
  `rah_auth(api_key = "stupid things", verbose = TRUE)` threw an error with unexpected message.
  Expected match: "Authorization error: HTTP status code"
  Actual message: "Timeout was reached: [apiv2.ahrefs.com] Resolving timed out after 10001 milliseconds"
  Backtrace:
       █
    1. ├─testthat::expect_error(...) test_auth.R:10:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. └─RAhrefs::rah_auth(api_key = "stupid things", verbose = TRUE)
    7.   └─httr::GET(...)
    8.     └─httr:::request_perform(req, hu$handle$handle)
    9.       ├─httr:::request_fetch(req$output, req$url, handle)
   10.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   11.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
  Error: Test failures
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    htmlwidgets   9.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   7.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [238s/457s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randomsearch)
  Loading required package: ParamHelpers
  Loading required package: smoof
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/Rtmp1XaWUm/working_dir/RtmpT3aqNC/file393a4217c2b/2_15': no such file or directory
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_randomsearch.R:83:5): parallel randomsearch works with parallelMap ──
  Error: Errors occurred in 1 slave jobs, displaying at most 10 of them:
  
  00001: Error : [ENOENT] Failed to stat '/tmp/Rtmp1XaWUm/working_dir/RtmpT3aqNC/file393a4217c2b/2_15': no such file or directory
  
  
  Backtrace:
      █
   1. ├─randomsearch::randomsearch(...) test_randomsearch.R:83:4
   2. └─randomsearch:::randomsearch.smoof_function(...)
   3.   └─parallelMap::parallelMap(...)
   4.     └─parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5.       └─parallelMap:::stopWithJobErrorMessages(...)
   6.         └─BBmisc::stopf(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 69 ]
  Error: Test failures
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.6Mb
    etc    2.2Mb
    po     1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Running examples in ‘raveio-Ex.R’ failed
The error most likely occurred in:

> ### Name: LazyFST
> ### Title: R6 Class to Load 'fst' Files
> ### Aliases: LazyFST
> 
> ### ** Examples
> 
> 
> # Data to save, total 8 MB
> x <- matrix(rnorm(1000000), ncol = 100)
> 
> # Save to local disk
> f <- tempfile()
> fst::write_fst(as.data.frame(x), path = f)
> 
> # Load via LazyFST
> dat <- LazyFST$new(file_path = f, dims = c(10000, 100))
> 
> # dat < 1 MB
> pryr::object_size(dat)
22,720 B
> 
> # Check whether the data is identical
> range(dat[] - x)

 *** caught segfault ***
address 633acb22, cause 'memory not mapped'
Package suggested but not available for checking: ‘av’
Installation failed.
See ‘/home/ripley/R/packages/tests32/rbedrock.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rbiouml.Rnw’ using Sweave
Loading required package: RCurl
Loading required package: RJSONIO

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 5 
Error in queryJSON("/web/table/createTable", params = c(de = path, columns = toJSON(columns),  : 
  Error communicating with SQL server.

--- failed re-building ‘rbiouml.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.7Mb
    po    2.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback:
  File "<string>", line 1, in <module>
  File "/home/ripley/R/Lib32/reticulate/python/rpytools/loader.py", line 44, in _import_hook
    level=level

--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 84-94 (UsingReticulate.Rmd) 
Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback:
  File "/home/ripley/R/Lib32/reticulate/python/rpytools/loader.py", line 44, in _import_hook
    level=level

--- failed re-building ‘UsingReticulate.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppCNPy-intro.Rmd’ ‘UsingReticulate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppFarmHash.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    include   6.6Mb
Running ‘testthat.R’ [17s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-CSF.R:7:3): csf algorithm works ───────────────────────────────
  length(id_ground) %in% c(15459L, 15453L) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
PlotMST: no visible binding for global variable ‘X1’
PlotMST: no visible binding for global variable ‘X2’
PlotMST: no visible binding for global variable ‘label’
PlotMST: no visible binding for global variable ‘from.x’
PlotMST: no visible binding for global variable ‘to.x’
PlotMST: no visible binding for global variable ‘from.y’
PlotMST: no visible binding for global variable ‘to.y’
PlotMST: no visible binding for global variable ‘V1’
PlotMST: no visible binding for global variable ‘V2’
PlotPseudoTime: no visible binding for global variable ‘x’
PlotPseudoTime: no visible binding for global variable ‘y’
PlotPseudoTime: no visible binding for global variable ‘Timepoint’
PlotTrajectory: no visible binding for global variable ‘X1’
PlotTrajectory: no visible binding for global variable ‘X2’
PlotTrajectory: no visible binding for global variable ‘label’
PlotTrajectory: no visible binding for global variable ‘x’
PlotTrajectory: no visible binding for global variable ‘y’
Undefined global functions or variables:
  Timepoint V1 V2 X1 X2 from.x from.y label to.x to.y x y
'library' or 'require' call not declared from: ‘SingleCellExperiment’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: sf
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0

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

RCzechia: downloading remote dataset.
udunits database from /usr/local/share/udunits/udunits2.xml
RCzechia: downloading remote dataset.
RCzechia: downloading remote dataset.
Warning in st_centroid.sf(., brno) :
  st_centroid assumes attributes are constant over geometries of x
RCzechia: downloading remote dataset.
Loading required package: sp

Attaching package: 'raster'

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

    select

RCzechia: downloading remote dataset.
RCzechia: using temporary local dataset.
Quitting from lines 295-322 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Timeout was reached: [web.archive.org] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rdf_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   1.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.7Mb
    doc    2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ReDaMoR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.3Mb
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Package suggested but not available for checking: ‘rsolr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    arabb      1.0Mb
    doc        1.3Mb
    examples   2.0Mb
Running ‘testthat.R’ [19s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(retrosheet)
  
  For Retrosheet data obtained with this package:
  
  The information used here was obtained free of charge from
  and is copyrighted by Retrosheet. Interested parties may
  contact Retrosheet at "www.retrosheet.org"
  
  > 
  > test_check("retrosheet")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-rmarkdown.R:14:5): Can be used in rmarkdown ───────────────────
  `runAllChunks("test-rmarkdown.Rmd")` threw an error.
  Message: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Class:   simpleError/error/condition
  Backtrace:
      █
   1. ├─testthat::expect_error(runAllChunks("test-rmarkdown.Rmd"), NA) test-rmarkdown.R:14:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─retrosheet:::runAllChunks("test-rmarkdown.Rmd")
   7.   └─rmarkdown::render(rmd, output_file = tempR, quiet = TRUE) test-rmarkdown.R:10:8
   8.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   9.       └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 231-254 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 227-251 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
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    java   5.3Mb
installed size is  7.5Mb
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    doc       2.2Mb
    extdata   2.9Mb
installed size is  8.2Mb
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    doc        3.5Mb
    misc       1.1Mb
    pictures   1.5Mb
Running examples in ‘rGEDI-Ex.R’ failed
The error most likely occurred in:

> ### Name: clipLevel1BGeo
> ### Title: Clip GEDI Full Waveform Geolocations by Coordinates
> ### Aliases: clipLevel1BGeo
> 
> ### ** Examples
> 
> # Specifying the path to GEDI level1B data (zip file)
> outdir = tempdir()
> level1B_fp_zip <- system.file("extdata",
+                   "GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip",
+                   package="rGEDI")
> 
> # Unzipping GEDI level1B data
> level1Bpath <- unzip(level1B_fp_zip,exdir = outdir)
> 
> # Reading GEDI level1B data (h5 file)
> level1b<-readLevel1B(level1Bpath=level1Bpath)
> 
> # Extracting GEDI Full Waveform Geolocations
> level1bGeo<-getLevel1BGeo(level1b)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   2%Error in self$read_low_level(file_space = self_space_id, mem_space = mem_space_id,  : 
  HDF5-API Errors:
    error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
        class: HDF5
        major: Invalid arguments to routine
        minor: Inappropriate type
Calls: getLevel1BGeo ... assign -> [ -> [.H5D -> <Anonymous> -> <Anonymous> -> .Call
Execution halted
installed size is  5.4Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v7.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
Loading required package: date
Loading required package: vars
Loading required package: MASS
Loading required package: strucchange
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: urca
Loading required package: lmtest

Attaching package: 'vars'

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

    A

Loading required package: blockmatrix
Loading required package: Matrix
Loading required package: stringr

Attaching package: 'stringr'

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

    boundary


Attaching package: 'lubridate'

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

    days, hours, minutes, seconds, years

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

    interval

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

    date, intersect, setdiff, union

Quitting from lines 50-63 (precipitation_stochastic_generation_v7.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v7.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘precipitation_stochastic_generation_v7.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v7.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘rgeoprofile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 141-142 (rgeoprofile.Rmd) 
Error: processing vignette 'rgeoprofile.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rgeoprofile.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
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    doc     1.8Mb
    fonts   1.6Mb
    libs    1.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_rhandsontable.Rmd’

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

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

> ### Name: datamuse_api
> ### Title: Call Datamuse API and return data.
> ### Aliases: datamuse_api
> 
> ### ** Examples
> 
> datamuse_api("/words?rel_rhy=test")
Error: Datamuse API request failed [503]
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-rhymer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-38 (intro-to-rhymer.Rmd) 
Error: processing vignette 'intro-to-rhymer.Rmd' failed with diagnostics:
Datamuse API request failed [503]
--- failed re-building ‘intro-to-rhymer.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-rhymer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (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. 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.
installed size is 11.2Mb
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installed size is 26.0Mb
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installed size is 10.2Mb
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installed size is  5.4Mb
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installed size is  5.9Mb
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    templates   5.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-144 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
res$response_headers$`content-type` == "application/json;charset=UTF-8" is not TRUE
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
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    data   2.9Mb
    doc    1.8Mb
installed size is 11.4Mb
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    R  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘robin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.7-0 (2021-06-25) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    det

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

    backsolve, forwardsolve

Loading required package: viridis
Loading required package: viridisLite
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Loading required package: qpdf
Quitting from lines 97-98 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘robin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
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    extdata   2.8Mb
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    R      1.3Mb
    data   2.8Mb
installed size is  5.3Mb
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    R   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rpolyhedra.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in snapshot3d(scene = x, width = width, height = height) :
  webshot = TRUE requires the webshot2 package; using rgl.snapshot() instead
Quitting from lines 49-88 (Rpolyhedra.Rmd) 
Error: processing vignette 'Rpolyhedra.Rmd' failed with diagnostics:
OpenGL is not available in this build
--- failed re-building ‘Rpolyhedra.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
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    doc   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  5.8Mb
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    R      1.3Mb
    libs   3.9Mb
Running ‘testthat.R’ [31m/38m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
installed size is 18.2Mb
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    R      1.8Mb
    doc    4.9Mb
    libs  10.8Mb
installed size is 13.2Mb
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    lib         1.4Mb
    libs        8.8Mb
    unitTests   1.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Running ‘testthat.R’ [691s/581s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rstyles)
  > library(mirt)
  Loading required package: stats4
  Loading required package: lattice
  > 
  > test_check("rstyles")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_sequential_mae5.R:38:3): Item parameters of sequential M, A, E RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((slopes[, 2] - estItemPars[, 2])^2) is not strictly less than 0.09. Difference: 0.00671
  ── Failure (test_simultaneous_aem.R:40:3): Item parameters of simultaneous A, E, M RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((slopes[, 1] - estItemPars[, 1])^2) is not strictly less than 0.2. Difference: 2.92
  ── Failure (test_simultaneous_aem.R:44:3): Item parameters of simultaneous A, E, M RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((intercepts[, 1] - estItemPars[, 26])^2) is not strictly less than 0.06. Difference: 0.0296
  ── Failure (test_simultaneous_aem.R:45:3): Item parameters of simultaneous A, E, M RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((intercepts[, 2] - estItemPars[, 27])^2) is not strictly less than 0.12. Difference: 0.161
  ── Failure (test_simultaneous_aem.R:46:3): Item parameters of simultaneous A, E, M RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((intercepts[, 3] - estItemPars[, 28])^2) is not strictly less than 0.09. Difference: 0.327
  ── Failure (test_simultaneous_aem.R:47:3): Item parameters of simultaneous A, E, M RS (with 5-point scale) recovers in estimation with reasonable MSEs. ──
  mean((intercepts[, 4] - estItemPars[, 29])^2) is not strictly less than 0.08. Difference: 0.612
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rsyncrosim_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (rsyncrosim_tutorial.Rmd) 
Error: processing vignette 'rsyncrosim_tutorial.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘rsyncrosim_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
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    R           1.4Mb
    bootstrap   1.8Mb
    data        2.3Mb
installed size is  5.1Mb
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    rmarkdown   4.9Mb
installed size is 11.0Mb
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    doc    7.9Mb
    libs   2.3Mb
installed size is  5.8Mb
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    R     3.1Mb
    doc   1.0Mb
installed size is  5.5Mb
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installed size is  5.6Mb
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installed size is  7.4Mb
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    libs      2.9Mb
installed size is  5.2Mb
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installed size is  6.7Mb
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    libs   4.1Mb
installed size is  6.2Mb
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    include   2.2Mb
    libs      2.9Mb
installed size is  5.2Mb
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    doc           3.3Mb
    htmlwidgets   1.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
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    bin  10.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.3Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'pogs'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    example   2.7Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    5.9Mb
installed size is  5.1Mb
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    docs      1.9Mb
    extdata   2.1Mb
installed size is  5.1Mb
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    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   1.0Mb
    help      2.5Mb
Package required but not available: ‘x13binary’

Package suggested but not available for checking: ‘seasonalview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
Package which this enhances but not available for checking: ‘rsvg’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    4.2Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.6Mb
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    data   4.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.3Mb
Package suggested but not available for checking: ‘monocle’
Running ‘testthat.R’ [117s/179s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Seurat)
  Attaching SeuratObject
  > 
  > test_check("Seurat")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • On CRAN (19)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_load_10X.R:34:1): (code run outside of `test_that()`) ───────────
  Error: HDF5-API Errors:
      error #000: H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  
  Backtrace:
      █
   1. └─Seurat::Load10X_Spatial(data.dir = "../testdata/visium") test_load_10X.R:34:0
   2.   └─Seurat::Read10X_h5(...)
   3.     ├─infile[[paste0(genome, "/", feature_slot)]][]
   4.     └─hdf5r:::`[.H5D`(...)
   5.       └─x$read(...)
   6.         └─self$read_low_level(...)
  
  [ FAIL 1 | WARN 9 | SKIP 19 | PASS 587 ]
  Error: Test failures
  Execution halted
Running examples in ‘sfarrow-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_sf_dataset
> ### Title: Read an Arrow multi-file dataset and create 'sf' object
> ### Aliases: read_sf_dataset
> 
> ### ** Examples
> 
> # read spatial object
> nc <- sf::st_read(system.file("shape/nc.shp", package="sf"), quiet = TRUE)
> 
> # create random grouping
> nc$group <- sample(1:3, nrow(nc), replace = TRUE)
> 
> # use dplyr to group the dataset. %>% also allowed
> nc_g <- dplyr::group_by(nc, group)
> 
> # write out to parquet datasets
> # partitioning determined by dplyr 'group_vars'
> write_sf_dataset(nc_g, path = file.path(tempdir(), "ds"))
Warning: This is an initial implementation of Parquet/Feather file support and
geo metadata. This is tracking version 0.1.0 of the metadata
(https://github.com/geopandas/geo-arrow-spec). This metadata
specification may change and does not yet make stability promises.  We
do not yet recommend using this in a production setting unless you are
able to rewrite your Parquet/Feather files.
Error in all_record_batches(dots) : 
  Cannot call all_record_batches(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries. 
Calls: write_sf_dataset -> <Anonymous> -> all_record_batches
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example_sfarrow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-54 (example_sfarrow.Rmd) 
Error: processing vignette 'example_sfarrow.Rmd' failed with diagnostics:
Cannot call io___MemoryMappedFile__Open(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries. 
--- failed re-building ‘example_sfarrow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘v1_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 61-70 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
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    doc      2.5Mb
    sqlite   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 208-210 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

--- re-building ‘sf7.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sf7.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
X connection to :5.0 broken (explicit kill or server shutdown).
installed size is  7.5Mb
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    data   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
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installed size is  9.7Mb
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installed size is 17.0Mb
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installed size is  5.1Mb
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    data             1.3Mb
    shiny-examples   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Gadgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Gadgets.Rmd’

--- re-building ‘Single-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Single-Layout.Rmd’

--- re-building ‘Split-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Split-Layout.Rmd’

--- re-building ‘Tabs-Layout.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Tabs-Layout.Rmd’

--- re-building ‘shinyMobile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-14 (shinyMobile.Rmd) 
Error: processing vignette 'shinyMobile.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘shinyMobile.Rmd’

--- re-building ‘shinyMobile_tools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shinyMobile_tools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.6Mb
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    shinyApp  22.5Mb
installed size is 13.0Mb
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    www   9.9Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
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    www    9.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
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installed size is  5.1Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘simplevis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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: Removed 2 rows containing non-finite values (stat_density).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
`summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'sex'. You can override using the `.groups` argument.
Quitting from lines 290-292 (simplevis.Rmd) 
Error: processing vignette 'simplevis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘simplevis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simrec-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 155-198 (simrec-vignette.Rmd) 
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘simrec-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘skm-vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <42> run based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.0Mb
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installed size is  5.0Mb
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    extdata   1.6Mb
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    R     1.4Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘crypto101.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'crypto101.rmd' failed with diagnostics:
The file crypto101.md is not encoded in UTF-8. These lines contain invalid UTF-8 characters: 67
--- failed re-building ‘crypto101.rmd’

--- re-building ‘intro.rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.rmd’

SUMMARY: processing the following file failed:
  ‘crypto101.rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
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    data   1.6Mb
    doc    2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘built_in.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘built_in.Rmd’

--- re-building ‘cloning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘cloning.Rmd’

--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 85-86 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘understanding_sortable_js.Rmd’

--- re-building ‘using_custom_css.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘using_custom_css.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

Identifing all possible orderings..
Total run time: 3.19 secs
Identifing all possible orderings..
Total run time: 1.61 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running examples in ‘spamtree-Ex.R’ failed
The error most likely occurred in:

> ### Name: spamtree
> ### Title: Bayesian Spatial Multivariate Tree GP Regression
> ### Aliases: spamtree
> 
> ### ** Examples
> 
> 
> # toy example with tiny dataset and short MCMC
> # on a univariate outcome
> 
> library(magrittr)
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(ggplot2)
> library(spamtree)
> 
> set.seed(2021)
> 
> SS <- 15 
> n <- SS^2 # total n. locations, including missing ones
> 
> coords <- data.frame(Var1=runif(n), Var2=runif(n)) %>%
+   as.matrix()
> 
> # generate data
> sigmasq <- 2.3
> phi <- 6
> tausq <- .1
> B <- c(-1,.5,1)
> 
> CC <- sigmasq * exp(-phi * as.matrix(dist(coords)))
> LC <- t(chol(CC))
> w <- LC %*% rnorm(n)
> p <- length(B)
> X <- rnorm(n * p) %>% matrix(ncol=p)
> y <- X %*% B + w + tausq^.5 * rnorm(n)
> 
> set_missing <- rbinom(n, 1, 0.1)
> 
> simdata <- data.frame(coords,
+                       y_full = y,
+                       w_latent = w) %>%
+   mutate(y_observed = ifelse(set_missing==1, NA, y_full))
> 
> # MCMC setup
> mcmc_keep <- 300
> mcmc_burn <- 300
> mcmc_thin <- 1
> 
> ybar <- mean(y, na.rm=TRUE)
> 
> # fit spamtree with defaults
> spamtree_done <- spamtree(y - ybar, X, coords, 
+           mcmc = list(keep=mcmc_keep, burn=mcmc_burn, thin=mcmc_thin), 
+           num_threads = 1)

 *** caught segfault ***
address 9d9dfc1c, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
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    R      1.8Mb
    java   3.8Mb
installed size is  5.5Mb
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    help   2.1Mb
installed size is  7.9Mb
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    R      3.4Mb
    help   3.2Mb
    libs   1.0Mb
installed size is  7.3Mb
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    shapes   3.9Mb
installed size is  6.5Mb
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installed size is 10.2Mb
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    R     1.4Mb
    doc   6.4Mb
    etc   1.5Mb
Running examples in ‘spdep-Ex.R’ failed
The error most likely occurred in:

> ### Name: nb2listwdist
> ### Title: Distance-based spatial weights for neighbours lists
> ### Aliases: nb2listwdist
> ### Keywords: spatial
> 
> ### ** Examples
> 
> # World examples
> data(world, package="spData")
> # neighbours on distance interval [0, 1000] kilometres
> pts <- st_centroid(st_transform(world, 3857))
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: st_centroid ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
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installed size is  5.4Mb
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File ‘sqp/libs/sqp.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Object: ‘solver_dense.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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
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installed size is  5.0Mb
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    doc    1.7Mb
    help   1.5Mb
installed size is  7.5Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘staple_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    2.9Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc   2.6Mb
    nc    4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘differences-gw-cow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘differences-gw-cow.Rmd’

--- re-building ‘statelists.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (statelists.Rmd) 
Error: processing vignette 'statelists.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘statelists.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    help   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting_Started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 206-208 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Getting_Started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.3Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
there is no package called 'seasonal'
--- failed re-building ‘stRvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shinygains.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shinygains.Rmd’

--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.8Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  11.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.9Mb
    help   1.0Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.9Mb
    doc    4.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    extdata   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘table1-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'table1'

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

    units, units<-

Quitting from lines 515-519 (table1-examples.Rmd) 
Error: processing vignette 'table1-examples.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘table1-examples.Rmd’

--- re-building ‘table1-latex.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'flextable'

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

    as_image, footnote


Attaching package: 'table1'

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

    units, units<-

--- finished re-building ‘table1-latex.Rmd’

SUMMARY: processing the following file failed:
  ‘table1-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    help   4.6Mb
Namespace in Imports field not imported from: ‘taxa’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc  11.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    telemac   1.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   3.6Mb
Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.1Mb
installed size is  9.2Mb
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    data   1.3Mb
    rda    7.7Mb
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘tidySEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: run_mx
> ### Title: Run as OpenMx model with sensible defaults
> ### Aliases: run_mx
> 
> ### ** Examples
> 
> df <- iris[1:3]
> names(df) <- paste0("X_", 1:3)
> run_mx(measurement(tidy_sem(df), meanstructure = TRUE))
Running model with 9 parameters
Error: C stack usage  287806612 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
Package suggested but not available for checking: ‘SingleR’
Namespaces in Imports field not imported from:
  ‘brio’ ‘curl’ ‘diffobj’ ‘gitcreds’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’
  ‘usethis’ ‘waldo’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_tidyusda.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-89 (using_tidyusda.Rmd) 
Error: processing vignette 'using_tidyusda.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^

--- failed re-building ‘using_tidyusda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running examples in ‘tmap-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_xlab
> ### Title: Axis labels
> ### Aliases: tm_xlab tm_ylab
> 
> ### ** Examples
> 
> data(World)
> 
> qtm(World, fill="#FFF8DC", projection=4326, inner.margins=0) +
+ 	tm_grid(x = seq(-180, 180, by=20), y=seq(-90,90,by=10), col = "gray70") +
+ 	tm_xlab("Longitude") +
+ 	tm_ylab("Latitude")
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: <Anonymous> ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tmap-JSS-code.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tmap-JSS-code.Rmd’

--- re-building ‘tmap-changes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.4, GDAL 2.2.4, PROJ 5.2.0
--- finished re-building ‘tmap-changes.Rmd’

--- re-building ‘tmap-getstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 68-79 (tmap-getstarted.Rmd) 
Error: processing vignette 'tmap-getstarted.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
--- failed re-building ‘tmap-getstarted.Rmd’

SUMMARY: processing the following file failed:
  ‘tmap-getstarted.Rmd’

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

> ### Name: crop_shape
> ### Title: Crop shape object
> ### Aliases: crop_shape
> 
> ### ** Examples
> 
> if (require(tmap) && packageVersion("tmap") >= "2.0") {
+     data(World, NLD_muni, land, metro)
+ 
+     #land_NLD <- crop_shape(land, NLD_muni)
+ 
+     #qtm(land_NLD, raster="trees", style="natural")
+ 
+     metro_Europe <- crop_shape(metro, World[World$continent == "Europe", ], polygon = TRUE)
+ 
+     qtm(World) +
+     tm_shape(metro_Europe) +
+     	tm_bubbles("pop2010", col="red", title.size="European cities") +
+     	tm_legend(frame=TRUE)
+ }
Loading required package: tmap
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: crop_shape ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘polling_districts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-79 (polling_districts.Rmd) 
Error: processing vignette 'polling_districts.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
--- failed re-building ‘polling_districts.Rmd’

--- re-building ‘tongfen-ca-estimate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen-ca-estimate.Rmd’

--- re-building ‘tongfen.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen.Rmd’

--- re-building ‘tongfen_ca.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen_ca.Rmd’

--- re-building ‘tongfen_us.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘tongfen_us.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘toOrdinal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    R      4.7Mb
    help   1.6Mb
    libs  14.8Mb
Package suggested but not available for checking: ‘moveVis’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix
Loading required package: fds
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is 13.4Mb
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    doc    4.0Mb
    libs   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-137 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_rosenbrock.R:67:9): Rosenbrock ────────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  Backtrace:
      █
   1. └─testthat::expect_match(opt0$status, "Success") test_rosenbrock.R:67:8
   2.   └─testthat:::expect_match_(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 15 ]
  Error: Test failures
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   4.6Mb
installed size is  5.3Mb
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    doc     1.5Mb
    fonts   2.9Mb
installed size is 10.9Mb
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    doc     7.3Mb
    ubinc   2.5Mb
installed size is  5.2Mb
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    R      1.6Mb
    libs   2.9Mb
installed size is  6.9Mb
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    data       1.0Mb
    doc        1.1Mb
    shinyapp   4.1Mb
installed size is  7.3Mb
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    doc         1.7Mb
    dummydata   1.5Mb
    libs        2.0Mb
installed size is  5.4Mb
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    data      2.0Mb
    extdata   2.6Mb
Package suggested but not available for checking: ‘TSstudio’
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    libs   1.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   6.6Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘varrank.Rmd’ using knitr
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    margin

Loading required package: parallel
Quitting from lines 122-125 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
--- failed re-building ‘varrank.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_vegalite.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘intro_to_vegalite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    help   3.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    help          1.8Mb
    htmlwidgets   6.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-visNetwork.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CDISC_ADaM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘CDISC_ADaM.Rmd’

--- re-building ‘Consort_flow_diagram.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Consort_flow_diagram.Rmd’

--- re-building ‘Styling_KM_plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘Styling_KM_plots.Rmd’

--- re-building ‘Time_to_event_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-105 (Time_to_event_analysis.Rmd) 
Error: processing vignette 'Time_to_event_analysis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Time_to_event_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gg_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
--- finished re-building ‘gg_vistime-vignette.Rmd’

--- re-building ‘hc_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-41 (hc_vistime-vignette.Rmd) 
Error: processing vignette 'hc_vistime-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hc_vistime-vignette.Rmd’

--- re-building ‘vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 32-40 (vistime-vignette.Rmd) 
Error: processing vignette 'vistime-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vistime-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘hc_vistime-vignette.Rmd’ ‘vistime-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘shiny-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-63 (shiny-example.Rmd) 
Error: processing vignette 'shiny-example.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘shiny-example.Rmd’

SUMMARY: processing the following file failed:
  ‘shiny-example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    extdata   8.9Mb
Package suggested but not available for checking: ‘archive’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.3Mb
Package suggested but not available for checking: ‘rcdk’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(webex)
  > 
  > test_check("webex")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compilation.R:16:3): minimal compile ────────────────────────────
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
      █
   1. └─rmarkdown::render(tf, quiet = TRUE) test-compilation.R:16:2
   2.   └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
   3.     └─rmarkdown:::stop2(paste(msg, collapse = " "))
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 31 ]
  Error: Test failures
  Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
Can't join on `x$a2` x `y$a2` because of incompatible types.
ℹ `x$a2` is of type <logical>>.
ℹ `y$a2` is of type <character>>.
--- failed re-building ‘united_nations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bn   7.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘wordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Package suggested but not available for checking: ‘ROTS’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       3.4Mb
    extdata   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 row(s) containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

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


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘x13binary’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/x13binary.Rcheck/00install.out’ for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Found the following significant warnings:
  yakmo.h:184:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/ripley/R/packages/tests32/yakmoR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(balance)
  > 
  > test_check("balance")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-compute.R:3:1): (code run outside of `test_that()`) ─────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-compute.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-output.R:3:1): (code run outside of `test_that()`) ──────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-output.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-sort.R:3:1): (code run outside of `test_that()`) ────────────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-sort.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  ── Error (test-wide2long.R:3:1): (code run outside of `test_that()`) ───────────
  Error: there is no package called 'robCompositions'
  Backtrace:
      █
   1. └─utils::data(expenditures, package = "robCompositions") test-wide2long.R:3:0
   2.   └─base::find.package(package, lib.loc, verbose = verbose)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [9s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blaise)
  > 
  > test_check("blaise")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_types.R:164:3): empty STRING ──────────────────────────────────
  rep(NA_character_, 10) not equal to dfnew[["A"]].
  Lengths differ: 10 is not 1
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 419 ]
  Error: Test failures
  Execution halted
Found the following significant warnings:
  /usr/include/gtk-2.0/gtk/gtktypeutils.h:236:1: warning: ‘GTypeDebugFlags’ is deprecated [-Wdeprecated-declarations]
  /usr/include/gtk-2.0/gtk/gtktooltips.h:73:3: warning: ‘GTimeVal’ is deprecated: Use 'GDateTime' instead [-Wdeprecated-declarations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cairoDevice.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Discriminant_analysis_examples.Rmd’ using knitr
Quitting from lines 360-369 (Discriminant_analysis_examples.Rmd) 
Error: processing vignette 'Discriminant_analysis_examples.Rmd' failed with diagnostics:
cannot open the connection to ‘https://www.lancaster.ac.uk/staff/taylorb1/mnist.RData’
--- failed re-building ‘Discriminant_analysis_examples.Rmd’

--- re-building ‘K_nearest_neighbors_examples.Rmd’ using knitr
--- finished re-building ‘K_nearest_neighbors_examples.Rmd’

--- re-building ‘Neural_net_examples.Rmd’ using knitr
--- finished re-building ‘Neural_net_examples.Rmd’

--- re-building ‘Random_forest_examples.Rmd’ using knitr
--- finished re-building ‘Random_forest_examples.Rmd’

--- re-building ‘Rpart_examples.Rmd’ using knitr
--- finished re-building ‘Rpart_examples.Rmd’

--- re-building ‘Support_vector_machine_examples.Rmd’ using knitr
--- finished re-building ‘Support_vector_machine_examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_v_fmt
> ### Title: Adds variable format information to a tibble
> ### Aliases: add_v_fmt
> 
> ### ** Examples
> 
> 
> # Extract file path for sample ecotype file
> sample_eco_file <- system.file('extdata','SAMPLE.ECO',package='DSSAT')
> 
> # Read sample ecotype file
> eco <- read_eco(sample_eco_file)
Error: '@ECO#  ECONAME.........  TBASE  TOPT ROPT   P20  DJTI  GDDE  DSGFT  RUE   KCAN  TSEN  CDAY' does not exist in current working directory ('/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DSSAT.Rcheck').
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown

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


Attaching package: 'lubridate'

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

    date, intersect, setdiff, union

Quitting from lines 59-61 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
'This file was created by CMPT_ME_BEME_OP_INV_RETS using the 202105 CRSP database.' does not exist in current working directory ('/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/frenchdata.Rcheck/vign_test/frenchdata/vignettes').
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fRLR.Rnw’ using Sweave
Warning: stack imbalance in 'withVisible', 33 then 35
Timing stopped at: 0.054 0 0.029

Error: processing vignette 'fRLR.Rnw' failed with diagnostics:
 chunk 4 
Error in try(withVisible(eval(expr, .GlobalEnv)), silent = TRUE) : 
  R_Reprotect: only -717 protected items, can't reprotect index -718

--- failed re-building ‘fRLR.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: genius_lyrics
> ### Title: Retrieve song lyrics from Genius.com
> ### Aliases: genius_lyrics
> 
> ### ** Examples
> 
> genius_lyrics(artist = "Kendrick Lamar", song = "Money Trees")
Warning: `html_session()` was deprecated in rvest 1.0.0.
Please use `session()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
# A tibble: 111 × 3
   track_title  line lyric                                                      
   <chr>       <int> <chr>                                                      
 1 Money Trees     1  <NA>                                                      
 2 Money Trees     2 "Uh, me and my niggas tryna get it, ya bish (Ya bish)"     
 3 Money Trees     3 "Hit the house lick: tell me, is you wit' it, ya bish? (Ya…
 4 Money Trees     4 "Home invasion was persuasive (Was persuasive)"            
 5 Money Trees     5 "From nine to five I know it's vacant, ya bish (Ya bish)"  
 6 Money Trees     6 "Dreams of livin' life like rappers do (Like rappers do)"  
 7 Money Trees     7 "Back when condom wrappers wasn't cool (They wasn't cool)" 
 8 Money Trees     8 "I fucked Sherane and went to tell my bros (Tell my bros)" 
 9 Money Trees     9 "Then Usher Raymond \"Let It Burn\" came on (\"Let Burn\" …
10 Money Trees    10 "Hot sauce all in our Top Ramen, ya bish (Ya bish)"        
# … with 101 more rows
> genius_lyrics("JMSN", "Drinkin")
Error in if (length(res) == 0 || res == -1) { : 
  missing value where TRUE/FALSE needed
Calls: genius_lyrics ... <Anonymous> -> vroom_ -> <Anonymous> -> split_path_ext
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genius_basics.Rmd’ using rmarkdown

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

Quitting from lines 46-47 (genius_basics.Rmd) 
Error: processing vignette 'genius_basics.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘genius_basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mix.curves
> ### Title: Build a custom-made, mixed calibration curve.
> ### Aliases: mix.curves
> 
> ### ** Examples
> 
> mix.curves()
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/IntCal/extdata/mixed.14C': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: mix.curves -> write.table -> file
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:909:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘testthat.R’ [34s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test.match_on.R:591:5): standardization_scale with svyglm ────────────
  Error: non-numeric argument to binary operator
  Backtrace:
      █
   1. └─optmatch::standardization_scale(...) test.match_on.R:591:4
   2.   └─optmatch:::standardizer(des_t)
   3.     ├─stats::update(design, abs_dev = abs(design$variable$x - med))
   4.     └─survey:::update.survey.design(...)
   5.       └─base::eval(dots[[j]], object$variables, parent.frame())
   6.         └─base::eval(dots[[j]], object$variables, parent.frame())
  
  [ FAIL 1 | WARN 2 | SKIP 0 | PASS 1603 ]
  Error: Test failures
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bits.c:1247:23: warning: array subscript 8 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
  bits.c:1265:18: warning: array subscript 9 is outside array bounds of ‘unsigned int[1]’ [-Warray-bounds]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RDieHarder.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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.
Found the following significant warnings:
  Rserv.c:2150:3: warning: ‘RSA_generate_key’ is deprecated [-Wdeprecated-declarations]
  Rserv.c:816:4: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:817:3: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:820:22: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:821:22: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:372:2: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:375:3: warning: ignoring return value of ‘chown’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2342:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3351:4: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:3358:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2088:7: warning: ignoring return value of ‘setgid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  Rserv.c:2090:7: warning: ignoring return value of ‘setuid’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  oc.c:47:5: warning: ‘RAND_pseudo_bytes’ is deprecated [-Wdeprecated-declarations]
  standalone.c:220:3: warning: ignoring return value of ‘chdir’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rserve.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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. 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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_tidyusda.Rmd’ using rmarkdown
Quitting from lines 72-89 (using_tidyusda.Rmd) 
Error: processing vignette 'using_tidyusda.Rmd' failed with diagnostics:
GnuTLS recv error (-110): The TLS connection was non-properly terminated.
--- failed re-building ‘using_tidyusda.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABC.RAP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: processing vignette 'ABC.RAP.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘ABC.RAP.Rmd’

SUMMARY: processing the following file failed:
  ‘ABC.RAP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.9Mb
installed size is 83.7Mb
  sub-directories of 1Mb or more:
    libs  83.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABHgenotypeR-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (ABHgenotypeR-vignette.Rmd) 
Error: processing vignette 'ABHgenotypeR-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ABHgenotypeR-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rjags’

Package suggested but not available for checking: ‘INLA’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.5Mb
Packages required but not available: 'aroma.affymetrix', 'aroma.core'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ACSN-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 155-164 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘ACSN-vignette.Rmd’

--- re-building ‘ACSN_map_updating.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘ACSN_map_updating.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R  14.1Mb
Packages required but not available:
  'BSgenome', 'BSgenome.Hsapiens.UCSC.hg19', 'GenomicRanges'

Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm9',
  'BSgenome.Mmusculus.UCSC.mm10'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘EmpiricalBrownsMethod’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      █
   1. ├─testthat::expect_equal(...) test_merge_p_values.r:43:4
   2. │ └─testthat::quasi_label(enquo(expected), expected.label, arg = "expected")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::apply(...)
   5. │ └─ActivePathways:::FUN(newX[, i], ...)
   6. └─base::loadNamespace(x) test_merge_p_values.r:44:46
   7.   └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8.     └─base:::withOneRestart(expr, restarts[[1L]])
   9.       └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 71 ]
  Error: Test failures
  Execution halted
Package required but not available: ‘runjags’

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.
Packages required but not available: 'WGCNA', 'pcaMethods'

Package suggested but not available for checking: ‘DeconRNASeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 37-41 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘addScales.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 34-58 (addScales.Rmd) 
Error: processing vignette 'addScales.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘addScales.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    data       2.8Mb
    pictures   2.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    data    1.3Mb
    files   1.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘adegraphics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 222-223 (adegraphics.Rmd) 
Error: processing vignette 'adegraphics.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘adegraphics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data  10.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-68 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'HiTC', 'snpStats'
Package unavailable to check Rd xrefs: ‘snpStats’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘advclust.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 65-66 (advclust.Rmd) 
Error: processing vignette 'advclust.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘advclust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Package required but not available: ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘rjags’
Error(s) in re-building vignettes:
  ...
--- re-building ‘af_logit_exponential.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 181-189 (af_logit_exponential.Rmd) 
Error: processing vignette 'af_logit_exponential.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘af_logit_exponential.Rmd’

--- re-building ‘latentclass.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘latentclass.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘R2jags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Packages required but not available: 'miscF', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘agridat_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘agridat_data.Rmd’

--- re-building ‘agridat_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 39-59 (agridat_examples.Rmd) 
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘agridat_examples.Rmd’

--- re-building ‘agridat_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘agridat_intro.Rmd’

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

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

> ### Name: plotf
> ### Title: Plot to multiple devices
> ### Aliases: plotf
> ### Keywords: device
> 
> ### ** Examples
> 
>   x = runif(40)*4
>   y = x + runif(40)
>   plotf(expression(plot(x, y, type="p"))) # plots to active device only
>   plotf(xyplot(y~x), "myplot", type=c("active", "png", "pdf"), size=c(3,3))
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Error in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  : 
  polygon edge not found
Calls: plotf ... <Anonymous> -> widthDetails -> widthDetails.text -> grid.Call
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 147-160 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'R2jags', 'jagsUI'
Error(s) in re-building vignettes:
  ...
--- re-building ‘AIPW.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 69-81 (AIPW.Rmd) 
Error: processing vignette 'AIPW.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘AIPW.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘akc_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 90-92 (akc_vignette.Rmd) 
Error: processing vignette 'akc_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘akc_vignette.Rmd’

--- re-building ‘tutorial_raw_text.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-87 (tutorial_raw_text.Rmd) 
Error: processing vignette 'tutorial_raw_text.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tutorial_raw_text.Rmd’

SUMMARY: processing the following files failed:
  ‘akc_vignette.Rmd’ ‘tutorial_raw_text.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘akmedoids-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 386-422 (akmedoids-vignette.Rmd) 
Error: processing vignette 'akmedoids-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘akmedoids-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aldvmm_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 1030-1037 (aldvmm_vignette.Rmd) 
Error: processing vignette 'aldvmm_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘aldvmm_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘allestimates-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (allestimates-vignette.Rmd) 
Error: processing vignette 'allestimates-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘allestimates-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Package required but not available: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extdata   8.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 378-378 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 32.6Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
Running examples in ‘Andromeda-Ex.R’ failed
The error most likely occurred in:

> ### Name: Andromeda-class
> ### Title: The Andromeda class
> ### Aliases: Andromeda-class Andromeda show,Andromeda-method
> ###   $,Andromeda-method $<-,Andromeda-method [[<-,Andromeda-method
> ###   [[,Andromeda-method names,Andromeda-method length,Andromeda-method
> ###   close,Andromeda-method
> 
> ### ** Examples
> 
> andr <- andromeda(cars = cars, iris = iris)
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingAndromeda.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union
Error(s) in re-building vignettes:
--- re-building ‘andurinha.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 158-160 (andurinha.Rmd) 
Error: processing vignette 'andurinha.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘andurinha.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘activityGCMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    35.3Mb
Package suggested but not available for checking: ‘GEOquery’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   3.0Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/AntAngioCOOL.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [18s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `expected` is a logical vector (TRUE)
  ── Failure (test-prodStack.R:456:3): prodStack must work with refStudy, if interactive is set to TRUE and if x is a list of antaresDataList and refStudy an antaresDataList ,  ──
  isTRUE(...) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-prodStack.R:470:3): prodStack must work with refStudy, if interactive is set to TRUE and if x is a list of antaresDataList and refStudy an antaresDataList ,  ──
  all.equal(...) is not TRUE
  
  `actual` is a character vector ('Mean absolute difference: 2500')
  `expected` is a logical vector (TRUE)
  
  [ FAIL 12 | WARN 1 | SKIP 13 | PASS 290 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘access_inequality.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
udunits database from /Volumes/Builds/packages/big-sur-arm64/Rlib/4.1/units/share/udunits/udunits2.xml
Using year 2019
Using mode public_transport
Using year 2019
Using year 2010
Quitting from lines 48-61 (access_inequality.Rmd) 
Error: processing vignette 'access_inequality.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘access_inequality.Rmd’

--- re-building ‘access_maps.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
Using year 2019
Using mode public_transport
Using year 2019
Using year 2010
Quitting from lines 47-55 (access_maps.Rmd) 
Error: processing vignette 'access_maps.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘access_maps.Rmd’

--- re-building ‘intro_to_aopdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘intro_to_aopdata.Rmd’

--- re-building ‘landuse_maps.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Linking to GEOS 3.9.1, GDAL 3.2.3, PROJ 7.2.1
Using year 2019
Using year 2010
Quitting from lines 46-52 (landuse_maps.Rmd) 
Error: processing vignette 'landuse_maps.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘landuse_maps.Rmd’

SUMMARY: processing the following files failed:
  ‘access_inequality.Rmd’ ‘access_maps.Rmd’ ‘landuse_maps.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is 341.3Mb
  sub-directories of 1Mb or more:
    libs  340.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.3Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘apexcharter.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘apexcharter.Rmd’

--- re-building ‘chart-options.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘chart-options.Rmd’

--- re-building ‘facets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-56 (facets.Rmd) 
Error: processing vignette 'facets.Rmd' failed with diagnostics:
'options' must be a fully named list, or have no names (NULL)
--- failed re-building ‘facets.Rmd’

--- re-building ‘shiny-integration.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny-integration.Rmd’

--- re-building ‘spark-box.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘spark-box.Rmd’

--- re-building ‘sync-charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘sync-charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ggtree’
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error in loadNamespace(x) : there is no package called ‘ggtree’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘binary-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 72-76 (binary-data.Rmd) 
Error: processing vignette 'binary-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘binary-data.Rmd’

--- re-building ‘continuous-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'AmesHousing'

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

    ames_new

Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'recipes'

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

    step

Quitting from lines 140-142 (continuous-data.Rmd) 
Error: processing vignette 'continuous-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘continuous-data.Rmd’

SUMMARY: processing the following files failed:
  ‘binary-data.Rmd’ ‘continuous-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘apsimx-scripts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘apsimx-scripts.Rmd’

--- re-building ‘apsimx.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 119-123 (apsimx.Rmd) 
Error: processing vignette 'apsimx.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘apsimx.Rmd’

--- re-building ‘optim-apsim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 85-102 (optim-apsim.Rmd) 
Error: processing vignette 'optim-apsim.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘optim-apsim.Rmd’

SUMMARY: processing the following files failed:
  ‘apsimx.Rmd’ ‘optim-apsim.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 8-20 (./../man/rmdhunks/linelist-example.Rmd) 
Quitting from lines 46-47 (./../man/rmdhunks/linelist-example.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AQuadtreeUse.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning: `summarise_()` was deprecated in dplyr 0.7.0.
Please use `summarise()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Arial"
Quitting from lines 104-109 (AQuadtreeUse.Rmd) 
Error: processing vignette 'AQuadtreeUse.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘AQuadtreeUse.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘RBGL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘arctools_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

    hour, isoweek, mday, minute, month, quarter, second, wday, week,
    yday, year

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

    date, intersect, setdiff, union

Quitting from lines 60-67 (arctools_intro.Rmd) 
Error: processing vignette 'arctools_intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘arctools_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘arena2r-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 79-84 (arena2r-vignette.Rmd) 
Error: processing vignette 'arena2r-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘arena2r-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘arena2r-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'qvalue', 'ComplexHeatmap'

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

Packages suggested but not available for checking:
  'affxparser', 'affyPLM', 'aroma.light', 'gcrma', 'oligo',
  'oligoClasses', 'pdInfoBuilder', 'AffymetrixDataTestFiles'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: 'aroma.core', 'PSCBS'

Packages suggested but not available for checking: 'aroma.light', 'GLAD'

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

Packages suggested but not available for checking:
  'EBImage', 'aroma.light', 'GLAD', 'sfit', 'expectile', 'HaarSeg',
  'mpcbs'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs  49.2Mb
installed size is 92.8Mb
  sub-directories of 1Mb or more:
    libs  91.8Mb
Error(s) in re-building vignettes:
--- re-building ‘art-contrasts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: car
Loading required package: carData

Attaching package: 'car'

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

    recode

Quitting from lines 106-122 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘art-contrasts.Rmd’

--- re-building ‘art-effect-size.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Loading required package: carData

Attaching package: 'car'

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

    Recode

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

    recode

Quitting from lines 168-179 (art-effect-size.Rmd) 
Error: processing vignette 'art-effect-size.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘art-effect-size.Rmd’

SUMMARY: processing the following files failed:
  ‘art-contrasts.Rmd’ ‘art-effect-size.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.8Mb
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Class: 
  Default Class: setosa
  Number of rules: 9
  Classification method: weighted by laplace - using best 5 rules
  Description: FOIL-based classifier (Yin and Han, 2003)
  
  Accuracy: 0.953 
  CBA Classifier Object
  Class: 
  Default Class: NA
  Number of rules: 9
  Classification method: logit  
  Description: RCAR+ based on RCAR (Azmi et al., 2019)
  
  Accuracy: 0.96
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/arulesNBMiner.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 101-125 (adaptive_shrinkage.Rmd) 
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘adaptive_shrinkage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/aslib.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘AssetCorr_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 80-85 (AssetCorr_vignette.Rmd) 
Error: processing vignette 'AssetCorr_vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘AssetCorr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  isoscape.iso[, 1]   0.2512     0.3655   0.687   0.4994  
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  Residual standard error: 4.039 on 21 degrees of freedom
  Multiple R-squared:  0.02201,	Adjusted R-squared:  -0.02457 
  F-statistic: 0.4725 on 1 and 21 DF,  p-value: 0.4994
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_plot.QA.R:31:3): QA and plot.QA work ──────────────────────────
  `plot.QA(qa1, outDir = tempdir())` produced warnings.
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 96 ]
  Error: Test failures
  Execution halted
Packages suggested but not available for checking:
  'asteRiskData', 'BiocStyle'
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-58 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
boundary (singular) fit: see ?isSingular
fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
boundary (singular) fit: see ?isSingular
Quitting from lines 344-353 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Freiburger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 24-30 (Freiburger.Rmd) 
Error: processing vignette 'Freiburger.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Freiburger.Rmd’

--- re-building ‘Intro_to_PTA_Standards.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (Intro_to_PTA_Standards.Rmd) 
Error: processing vignette 'Intro_to_PTA_Standards.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Intro_to_PTA_Standards.Rmd’

SUMMARY: processing the following files failed:
  ‘Freiburger.Rmd’ ‘Intro_to_PTA_Standards.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  au.c:222:8: warning: 'AudioHardwareGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:229:8: warning: 'AudioDeviceGetProperty' is deprecated: first deprecated in macOS 10.6 [-Wdeprecated-declarations]
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/audio.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using knitr
Quitting from lines 72-79 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘start_guide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
Loading required package: maps
Loading required package: mapdata
Quitting from lines 95-97 (start_guide.Rmd) 
Error: processing vignette 'start_guide.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘start_guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Packages required but not available:
  'siggenes', 'fgsea', 'org.Hs.eg.db', 'ConsensusClusterPlus',
  'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘finding-thresholds.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 43-49 (finding-thresholds.Rmd) 
Error: processing vignette 'finding-thresholds.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘finding-thresholds.Rmd’

--- re-building ‘thresholding-image-stacks.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘thresholding-image-stacks.Rmd’

--- re-building ‘thresholding-images.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘thresholding-images.Rmd’

SUMMARY: processing the following file failed:
  ‘finding-thresholds.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how-to-analyze-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-60 (how-to-analyze-data.Rmd) 
Error: processing vignette 'how-to-analyze-data.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘how-to-analyze-data.Rmd’

SUMMARY: processing the following file failed:
  ‘how-to-analyze-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘full-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 421-423 (full-example.Rmd) 
Error: processing vignette 'full-example.Rmd' failed with diagnostics:
replacement has length zero
--- failed re-building ‘full-example.Rmd’

SUMMARY: processing the following file failed:
  ‘full-example.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘a_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘a_intro.Rmd’

--- re-building ‘b_analyze-hass-cntry.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 42-64 (b_analyze-hass-cntry.Rmd) 
Error: processing vignette 'b_analyze-hass-cntry.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘b_analyze-hass-cntry.Rmd’

--- re-building ‘b_analyze-hass-region.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 59-87 (b_analyze-hass-region.Rmd) 
Error: processing vignette 'b_analyze-hass-region.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘b_analyze-hass-region.Rmd’

--- re-building ‘b_analyze-hass.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 44-66 (b_analyze-hass.Rmd) 
Error: processing vignette 'b_analyze-hass.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘b_analyze-hass.Rmd’

SUMMARY: processing the following files failed:
  ‘b_analyze-hass-cntry.Rmd’ ‘b_analyze-hass-region.Rmd’
  ‘b_analyze-hass.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘aweSOM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 122-123 (aweSOM.Rmd) 
Error: processing vignette 'aweSOM.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘aweSOM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/AWR.Athena.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/AWR.Kinesis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/AWR.KMS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/AWR.Rcheck/00install.out’ for details.
Package required but not available: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘babsim-vignette-introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 157-159 (babsim-vignette-introduction.Rmd) 
Error: processing vignette 'babsim-vignette-introduction.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘babsim-vignette-introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   3.3Mb
    libs   3.6Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Error(s) in re-building vignettes:
  ...
--- re-building ‘bacon.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 54-60 (bacon.Rmd) 
Error: processing vignette 'bacon.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘bacon.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 105.7Mb
  sub-directories of 1Mb or more:
    libs  104.0Mb
Package suggested but not available for checking: ‘philr’
Error(s) in re-building vignettes:
  ...
--- re-building ‘balance.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (balance.Rmd) 
Error: processing vignette 'balance.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘balance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Packages required but not available: 'rjags', 'R2jags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   1.8Mb
Package unavailable to check Rd xrefs: ‘rjags’
Packages required but not available: 'rjags', 'runjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: 'sva', 'affyPLM'

Package suggested but not available for checking: ‘ArrayExpress’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/bartMachineJARs.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/bartMachine.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘baRulho_quantifying_sound_degradation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: warbleR
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds

NOTE: functions have been renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Loading required package: viridisLite
Quitting from lines 996-1007 (baRulho_quantifying_sound_degradation.Rmd) 
Error: processing vignette 'baRulho_quantifying_sound_degradation.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
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    libs   3.9Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
prepare_Rd: no font could be found for family "Arial"
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/baseflow.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GO.db', 'GSEABase', 'org.Hs.eg.db', 'reactome.db'
Package required but not available: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/BASiNET.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BatchGetSymbols-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Warning in .getClassesFromCache(Class) :
  closing unused connection 4 (https://query1.finance.yahoo.com/v7/finance/download/abcdef?period1=1621987200&period2=1627171200&interval=1d&events=history&crumb=kndt78ujj6J)
Quitting from lines 67-73 (BatchGetSymbols-vignette.Rmd) 
Error: processing vignette 'BatchGetSymbols-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘BatchGetSymbols-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
installed size is 90.0Mb
  sub-directories of 1Mb or more:
    libs  87.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
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SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  44.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Packages required but not available: 'runjags', 'rjags'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 114.1Mb
  sub-directories of 1Mb or more:
    libs  112.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
--- re-building ‘bdpbinomial-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 121-123 (bdpbinomial-vignette.Rmd) 
Error: processing vignette 'bdpbinomial-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘bdpbinomial-vignette.Rmd’

--- re-building ‘bdplm-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 138-140 (bdplm-vignette.Rmd) 
Error: processing vignette 'bdplm-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘bdplm-vignette.Rmd’

--- re-building ‘bdpnormal-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 128-130 (bdpnormal-vignette.Rmd) 
Error: processing vignette 'bdpnormal-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘bdpnormal-vignette.Rmd’

--- re-building ‘bdpsurvival-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 191-193 (bdpsurvival-vignette.Rmd) 
Error: processing vignette 'bdpsurvival-vignette.Rmd' failed with diagnostics:
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--- failed re-building ‘bdpsurvival-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘bdpbinomial-vignette.Rmd’ ‘bdplm-vignette.Rmd’
  ‘bdpnormal-vignette.Rmd’ ‘bdpsurvival-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  14.8Mb
installed size is 102.3Mb
  sub-directories of 1Mb or more:
    libs  100.9Mb
installed size is 112.7Mb
  sub-directories of 1Mb or more:
    libs  111.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPV_NPV.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-78 (PPV_NPV.Rmd) 
Error: processing vignette 'PPV_NPV.Rmd' failed with diagnostics:
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--- failed re-building ‘PPV_NPV.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 61-68 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
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--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘PottsUtils’
installed size is  9.0Mb
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    data   2.7Mb
    libs   5.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘bayesmeta.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 139-140 (bayesmeta.Rmd) 
Error: processing vignette 'bayesmeta.Rmd' failed with diagnostics:
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--- failed re-building ‘bayesmeta.Rmd’

--- re-building ‘Roever2020-bayesmeta.pdf.asis’ using asis
--- finished re-building ‘Roever2020-bayesmeta.pdf.asis’

SUMMARY: processing the following file failed:
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Error: Vignette re-building failed.
Execution halted
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  26.5Mb
Packages suggested but not available for checking: 'cyjShiny', 'qtlnet'
Error(s) in re-building vignettes:
--- re-building ‘advanced.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 78-79 (advanced.Rmd) 
Error: processing vignette 'advanced.Rmd' failed with diagnostics:
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--- re-building ‘basic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘basic.Rmd’

--- re-building ‘default_ttests.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 55-59 (default_ttests.Rmd) 
Error: processing vignette 'default_ttests.Rmd' failed with diagnostics:
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--- re-building ‘plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 40-41 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
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SUMMARY: processing the following files failed:
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Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.9Mb
Packages suggested but not available for checking:
  'rjags', 'R2jags', 'runjags'
Found the following significant warnings:
  Warning: namespace ‘rjags’ is not available and has been replaced
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/BayesPostEst.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘R2jags’
Running examples in ‘BayesPostEst-Ex.R’ failed
The error most likely occurred in:

> ### Name: print.mcmcRocPrc
> ### Title: ROC and Precision-Recall Curves using Bayesian MCMC estimates
> ### Aliases: print.mcmcRocPrc plot.mcmcRocPrc as.data.frame.mcmcRocPrc
> ###   mcmcRocPrc mcmcRocPrc.default mcmcRocPrc.jags mcmcRocPrc.rjags
> ###   mcmcRocPrc.runjags mcmcRocPrc.stanfit mcmcRocPrc.stanreg
> ###   mcmcRocPrc.brmsfit mcmcRocPrc.bugs mcmcRocPrc.mcmc
> 
> ### ** Examples
> 
> # load simulated data and fitted model (see ?sim_data and ?jags_logit)
> data("jags_logit")
> 
> # using mcmcRocPrc
> fit_sum <- mcmcRocPrc(jags_logit,
+                       yname = "Y",
+                       xnames = c("X1", "X2"),
+                       curves = TRUE,
+                       fullsims = FALSE)
Error: Package "R2jags" is needed for this function to work. Please install it.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesPostEst)
  > 
  > test_check("BayesPostEst")
  Error in library(R2jags) : there is no package called 'R2jags'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
installed size is 13.6Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘conjugate-families.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-32 (conjugate-families.Rmd) 
Error: processing vignette 'conjugate-families.Rmd' failed with diagnostics:
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--- failed re-building ‘conjugate-families.Rmd’

--- re-building ‘model-evaluation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘model-evaluation.Rmd’

SUMMARY: processing the following file failed:
  ‘conjugate-families.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 20.1Mb
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    libs  17.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Package required but not available: ‘runjags’

Package suggested but not available for checking: ‘rjags’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    libs  37.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.8Mb
Package required but not available: ‘jagsUI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: 'R2jags', 'INLA'
Error(s) in re-building vignettes:
  ...
--- re-building ‘BClustLonG.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 62-69 (BClustLonG.Rmd) 
Error: processing vignette 'BClustLonG.Rmd' failed with diagnostics:
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--- failed re-building ‘BClustLonG.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'BRugs', 'rjags'
Error(s) in re-building vignettes:
  ...
--- re-building ‘BCSub.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (BCSub.Rmd) 
Error: processing vignette 'BCSub.Rmd' failed with diagnostics:
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--- failed re-building ‘BCSub.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdscale.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 52-53 (bdscale.Rmd) 
Error: processing vignette 'bdscale.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘bdscale.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘beadarray’

Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘cba_macsplex_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 31-38 (cba_macsplex_example.Rmd) 
Error: processing vignette 'cba_macsplex_example.Rmd' failed with diagnostics:
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--- failed re-building ‘cba_macsplex_example.Rmd’

--- re-building ‘legendplex_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 114-120 (legendplex_analysis.Rmd) 
Error: processing vignette 'legendplex_analysis.Rmd' failed with diagnostics:
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--- failed re-building ‘legendplex_analysis.Rmd’

--- re-building ‘preparing_flow_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘preparing_flow_data.Rmd’

SUMMARY: processing the following files failed:
  ‘cba_macsplex_example.Rmd’ ‘legendplex_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 105.8Mb
  sub-directories of 1Mb or more:
    libs  104.3Mb
Installation failed.
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.1/BeastJar.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'biomaRt', 'GEOquery'
Error(s) in re-building vignettes:
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

--- re-building ‘abcd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘complecs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘complecs.Rmd’

--- re-building ‘determinant-selection-table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘determinant-selection-table.Rmd’

--- re-building ‘determinant-selection-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 123-124 (determinant-selection-tutorial.Rmd) 
Error: processing vignette 'determinant-selection-tutorial.Rmd' failed with diagnostics:
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--- failed re-building ‘determinant-selection-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘determinant-selection-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘belg1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 48-60 (belg1.Rmd) 
Error: processing vignette 'belg1.Rmd' failed with diagnostics:
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--- failed re-building ‘belg1.Rmd’

SUMMARY: processing the following file failed:
  ‘belg1.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  49.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘benthos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.

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

Quitting from lines 335-342 (benthos.Rmd) 
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
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--- failed re-building ‘benthos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Package required but not available: ‘BiDAG’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs  60.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BetaPASS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 96-97 (BetaPASS.Rmd) 
Error: processing vignette 'BetaPASS.Rmd' failed with diagnostics:
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--- failed re-building ‘BetaPASS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.9Mb
    libs   7.1Mb
installed size is 152.8Mb
  sub-directories of 1Mb or more:
    include  152.8Mb
Package required but not available: ‘pcalg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  11.0Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Package suggested but not available for checking: ‘RODBC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 126-128 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      2.8Mb
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("bigmemory")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  • empty test (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_mwhich.R:34:5): mwhich recognizes NA ──────────────────────────
  mwhich(x, 1:2, NA, "eq", "OR") not identical to 1.
  Lengths differ: 0 is not 1
  ── Failure (test_mwhich.R:35:5): mwhich recognizes NA ──────────────────────────
  mwhich(x, 1:2, NA, "neq", "AND") not identical to as.numeric(2:10).
  Lengths differ: 10 is not 9
  
  [ FAIL 2 | WARN 1 | SKIP 7 | PASS 188 ]
  Error: Test failures
  Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs     12.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    help   1.5Mb
    libs   5.8Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Packages required but not available:
  'edgeR', 'Rsamtools', 'GenomicAlignments', 'GenomicRanges', 'csaw',
  'SummarizedExperiment'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 105.5Mb
  sub-directories of 1Mb or more:
    libs  105.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted