Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    2.2Mb
    tests   1.3Mb
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘robustbase’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  wrapper_Message.cpp:149:25: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
  wrapper_Message.cpp:253:49: warning: 'ByteSize' is deprecated: Please use ByteSizeLong() instead [-Wdeprecated-declarations]
See ‘/data/gannet/ripley/R/packages/tests-clang/RProtoBuf.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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.
Found the following significant warnings:
  rf.c:485:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RRF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mvMORPH’
  All declared Imports should be used.
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
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.
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.
Depends: includes the non-default packages:
  'biwt', 'cairoDevice', 'fBasics', 'gplots', 'gWidgets',
  'gWidgetsRGtk2', 'minerva', 'parmigene', 'stringr', 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

Requires orphaned package: ‘gplots’
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.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.
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 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
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.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘tcltk’ ‘tools’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/Rssa.Rcheck/00install.out’ for details.
installed size is 195.3Mb
  sub-directories of 1Mb or more:
    R       1.6Mb
    doc     4.5Mb
    libs  188.6Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
installed size is 181.0Mb
  sub-directories of 1Mb or more:
    libs  178.2Mb
installed size is 92.1Mb
  sub-directories of 1Mb or more:
    libs  90.8Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
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.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
File ‘rtfbs/libs/rtfbs.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  6.6Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.5Mb
    projects   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/RTransProb.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  19.5Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   2.2Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   7.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 53.8Mb
  sub-directories of 1Mb or more:
    libs  53.1Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 55.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     51.4Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'

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.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs    7.8Mb
    yacas   1.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs    8.5Mb
    yacas   1.6Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 40 (should be '.', not 'source'):
      source autobrew
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.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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 15.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs  12.4Mb
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘methods’
  All declared Imports should be used.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.4Mb
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.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
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.
File ‘SAPP/libs/SAPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 63.0Mb
  sub-directories of 1Mb or more:
    extdata  62.6Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
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.
File ‘sbfc/libs/sbfc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘sbrl/libs/sbrl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
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.
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
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.
Namespace in Imports field not imported from: ‘spData’
  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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/scio.Rcheck/00install.out’ for details.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
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.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/sdwd.Rcheck/00install.out’ for details.
File ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  7.9Mb
  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 18.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  15.3Mb
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'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘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’
plot.SEL: no visible global function definition for ‘plot’
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 plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SemNetCleaner’ ‘grid’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
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  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  13.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  24.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
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 16.1Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
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.
Packages suggested but not available for checking:
  'loomR', 'MAST', 'monocle'

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.

Suggests orphaned package: ‘SDMTools’
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   7.5Mb
Package unavailable to check Rd xrefs: ‘loomR’
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    libs     8.6Mb
    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 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
File ‘sharpData/libs/sharpData.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘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’ ‘getPass’ ‘svglite’ ‘websocket’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.3Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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.
Namespaces in Imports field not imported from:
  ‘coda’ ‘ellipse’ ‘viridis’
  All declared Imports should be used.
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.8Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
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  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.1Mb
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘metafor’
  All declared Imports should be used.
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  21.1Mb
Running examples in ‘SimuChemPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ###   character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ###   expected potency improvement, gaussian process
> 
> ### ** Examples
> 
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SimuChemPC
 --- call from context --- 
normalize(yTrain)
 --- call from argument --- 
if (class(x) == "data.frame") {
    sigma = sapply(x_norm, sd)
} else {
    sigma = sd(x_norm)
}
 --- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x) 
{
    mu = colMeans(x)
    x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
    if (class(x) == "data.frame") {
        sigma = sapply(x_norm, sd)
    }
    else {
        sigma = sd(x_norm)
    }
    sigma[sigma == 0] = 1
    norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
    return(list(norm, mu, sigma))
}
<bytecode: 0x5285930>
<environment: namespace:SimuChemPC>
 --- function search by body ---
Function normalize in namespace SimuChemPC has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
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 11.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   7.3Mb
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:
  ‘car’ ‘het.test’ ‘lmtest’ ‘lubridate’ ‘magrittr’ ‘tibble’ ‘tseries’
  All declared Imports should be used.
installed size is  6.4Mb
  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 33.5Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Running examples in ‘skyscapeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: reduct.compass
> ### Title: Data reduction for compass measurements
> ### Aliases: reduct.compass
> 
> ### ** Examples
> 
> loc <- c(35,-7)
> mag.az <- c(89.5, 105, 109.5)
> data <- reduct.compass(loc, mag.az, "2016/04/02")
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
skyscapeR
 --- call from context --- 
mag.dec(loc, date)
 --- call from argument --- 
if (class(loc) == "skyscapeR.horizon") {
    loc <- loc$georef
}
 --- R stacktrace ---
where 1: mag.dec(loc, date)
where 2: reduct.compass(loc, mag.az, "2016/04/02")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (loc, date) 
{
    if (class(loc) == "skyscapeR.horizon") {
        loc <- loc$georef
    }
    if (is.null(dim(loc))) {
        dim(loc) <- c(1, NROW(loc))
    }
    aux <- oce::magneticField(loc[, 2], loc[, 1], as.POSIXlt(date, 
        format = "%Y/%m/%d"))$declination
    return(aux)
}
<bytecode: 0xa8cfb38>
<environment: namespace:skyscapeR>
 --- function search by body ---
Function mag.dec in namespace skyscapeR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(loc) == "skyscapeR.horizon") { : 
  the condition has length > 1
Calls: reduct.compass -> mag.dec
Execution halted
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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   3.7Mb
Found the following significant warnings:
  slfm_MDN.cpp:26:38: warning: expression result unused [-Wunused-value]
  slfm_MNN.cpp:26:38: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/slfm.Rcheck/00install.out’ for details.
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.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Imports includes 36 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.

Requires orphaned package: ‘clues’
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.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  10.2Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/smoothSurv.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘SnowballC/libs/SnowballC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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   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.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 11.8Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.9Mb
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.
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  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  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.
File ‘spacejam/libs/spacejam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘spacodiR/libs/spacodiR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘rstudioapi’
  All declared Imports should be used.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  32.1Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
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.
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 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
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.
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 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
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:
  ‘dplyr’ ‘fasterize’
  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.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    data   4.7Mb
Note: found 25 marked Latin-1 strings
  Note: found 658 marked UTF-8 strings
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.2Mb
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.
File ‘spatstat.Knet/libs/spatstat.Knet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 18.5Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.2Mb
    libs   2.1Mb
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs  10.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
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  6.6Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
File ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Running examples in ‘SpecsVerification-Ex.R’ failed
The error most likely occurred in:

> ### Name: Detrend
> ### Title: Auxiliary function for removing trends and mean from observation
> ###   vector or ensemble matrix.
> ### Aliases: Detrend
> 
> ### ** Examples
> 
>  data(eurotempforecast)
>  Detrend(ens)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SpecsVerification
 --- call from context --- 
Detrend(ens)
 --- call from argument --- 
if (class(x) == "matrix") {
    xx <- rowMeans(x, na.rm = TRUE)
} else {
    xx <- x
}
 --- R stacktrace ---
where 1: Detrend(ens)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x, demean = TRUE) 
{
    if (class(x) == "matrix") {
        xx <- rowMeans(x, na.rm = TRUE)
    }
    else {
        xx <- x
    }
    N <- length(xx)
    if (N == 1) {
        trnd <- x
    }
    else {
        t <- 1:N
        lmod <- lm(xx ~ t)
        trnd <- drop(cbind(1, t) %*% coef(lmod))
    }
    m <- ifelse(demean, 0, mean(unlist(x), na.rm = TRUE))
    return(x - trnd + m)
}
<bytecode: 0x2637410>
<environment: namespace:SpecsVerification>
 --- function search by body ---
Function Detrend in namespace SpecsVerification has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "matrix") { : the condition has length > 1
Calls: Detrend
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
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 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘tibble’ ‘webshot’
  All declared Imports should be used.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘biomod2’
  All declared Imports should be used.
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
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Running examples in ‘squash-Ex.R’ failed
The error most likely occurred in:

> ### Name: corrogram
> ### Title: Draw a color-coded triangular matrix of pairwise correlations
> ### Aliases: corrogram
> ### Keywords: hplot
> 
> ### ** Examples
>  
>   
>   corrogram(cor(swiss), title = 'Pearson correlation')
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
squash
 --- call from context --- 
distogram(..., map = map)
 --- call from argument --- 
if (class(x) == "dist") x <- as.matrix(x)
 --- R stacktrace ---
where 1: distogram(..., map = map)
where 2: corrogram(cor(swiss), title = "Pearson correlation")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x, map, n = 10, base = NA, colFn = heat, key = TRUE, 
    title = NA, ...) 
{
    if (class(x) == "dist") 
        x <- as.matrix(x)
    stopifnot(nrow(x) == ncol(x))
    if (missing(map)) {
        map <- makecmap(x, n = n, base = base, colFn = colFn)
    }
    trianglegram(cmap(x, map = map), ...)
    if (key) 
        hkey(map = map, title = title)
    invisible(map)
}
<bytecode: 0x3e9c4f0>
<environment: namespace:squash>
 --- function search by body ---
Function distogram in namespace squash has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "dist") x <- as.matrix(x) : 
  the condition has length > 1
Calls: corrogram -> distogram
Execution halted
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Requires orphaned packages:
  ‘SDMTools’ ‘gplots’
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
possible bashism in configure line 19 ('command' with option other than -p):
  if [ $(command -v pkg-config) ]; then
  possible bashism in configure line 33 ($(OS|MACH)TYPE):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (alternative test command ([[ foo ]] should be [ foo ])):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 33 (should be 'b = a'):
  elif [[ "$OSTYPE" == "darwin"* ]]; then
  possible bashism in configure line 34 ('command' with option other than -p):
    if [ $(command -v brew) ]; then
  possible bashism in configure line 38 (should be '.', not 'source'):
      source autobrew
installed size is 73.2Mb
  sub-directories of 1Mb or more:
    libs  72.8Mb
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: ‘stabledist’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 13.3Mb
  sub-directories of 1Mb or more:
    include  10.3Mb
    lib       2.8Mb
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
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.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘mapproj’ ‘methods’
  All declared Imports should be used.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Imports includes 25 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.

Requires orphaned package: ‘gplots’
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘multigroup’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    data   2.4Mb
    libs   4.5Mb
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.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
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 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.4Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’
Namespaces in Imports field not imported from:
  ‘BSgenome’ ‘BiocManager’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
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.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  10.6Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.4Mb
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.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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 significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/SuperGauss.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceOptim’ ‘GPareto’ ‘rgenoud’
  All declared Imports should be used.
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.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    R      1.8Mb
    doc    2.3Mb
    libs   1.7Mb
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 142.2Mb
  sub-directories of 1Mb or more:
    libs  140.7Mb
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.
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    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
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
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.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘stats’ ‘survival’ ‘utils’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.2Mb
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.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.
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:
  ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘magrittr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  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  7.0Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
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:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘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.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘glmnet’ ‘quadprog’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
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.
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.

Requires orphaned package: ‘d3heatmap’
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   8.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  16.0Mb
Running examples in ‘TempleMetrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Fycondx.DR
> ### Title: Fycondx.DR
> ### Aliases: Fycondx.DR
> 
> ### ** Examples
> 
> data(igm)
> yvals <- seq(quantile(igm$lcfincome,.05,type=1),
+  quantile(igm$lcfincome,.95, type=1), length.out=100)
> dres <- distreg(lcfincome ~ lfincome + HEDUC, igm, yvals)
> xdf <- data.frame(lfincome=10, HEDUC=c("LessHS","HS"))
> d <- Fycondx(dres, yvals, xdf)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TempleMetrics
 --- call from context --- 
Fycondx.DR(dres, yvals, xdf)
 --- call from argument --- 
if (class(predmat) == "numeric") {
    predmat <- t(predmat)
}
 --- R stacktrace ---
where 1: Fycondx.DR(dres, yvals, xdf)
where 2: Fycondx(dres, yvals, xdf)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (object, yvals, xdf) 
{
    drobj <- object
    yvals <- drobj$yvals
    glmlist <- drobj$glmlist
    predmat <- sapply(glmlist, function(g) {
        predict(g, newdata = xdf, type = "response")
    })
    if (class(predmat) == "numeric") {
        predmat <- t(predmat)
    }
    out <- lapply(1:nrow(predmat), function(i) {
        makeDist(yvals, predmat[i, ], rearrange = TRUE)
    })
    out
}
<bytecode: 0x250aa78>
<environment: namespace:TempleMetrics>
 --- function search by body ---
Function Fycondx.DR in namespace TempleMetrics has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(predmat) == "numeric") { : 
  the condition has length > 1
Calls: Fycondx -> Fycondx.DR
Execution halted
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
possible bashism in configure line 34 ($(OS|MACH)TYPE):
    case "$OSTYPE" in "darwin"*)
  possible bashism in configure line 42 (should be '.', not 'source'):
      source autobrew
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.
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
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  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/text2vec.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.4Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
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  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    libs  14.9Mb
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  8.5Mb
  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:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’ ‘usethis’
  All declared Imports should be used.
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyxl.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.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.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Running examples in ‘tinter-Ex.R’ failed
The error most likely occurred in:

> ### Name: darken
> ### Title: Darken colour.
> ### Aliases: darken
> 
> ### ** Examples
> 
> darken(tinter("blue"), 0.2)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
tinter
 --- call from context --- 
check_colour(x)
 --- call from argument --- 
if (class(res) == "try-error") stop(x, " is not a valid color", 
    call. = FALSE)
 --- R stacktrace ---
where 1: check_colour(x)
where 2: tinter("blue")
where 3: lapply(x, check_colour)
where 4: darken(tinter("blue"), 0.2)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x) 
{
    res <- try(grDevices::col2rgb(x), silent = TRUE)
    if (class(res) == "try-error") 
        stop(x, " is not a valid color", call. = FALSE)
}
<bytecode: 0x13bd090>
<environment: namespace:tinter>
 --- function search by body ---
Function check_colour in namespace tinter has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(res) == "try-error") stop(x, " is not a valid color",  : 
  the condition has length > 1
Calls: darken -> lapply -> tinter -> check_colour
Execution halted
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
File ‘TKF/libs/TKF.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 ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    examples  14.2Mb
    include    3.0Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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   4.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.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.
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 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
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
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 13.6Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 116.4Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    libs  111.3Mb
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.
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.
Found the following significant warnings:
  rfmod.c:467:1: warning: expression result unused [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/trimTrees.Rcheck/00install.out’ for details.
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.
File ‘tripack/libs/tripack.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: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘htmltools’ ‘scales’ ‘stringr’
  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.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.5Mb
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.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
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.
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.
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  9.4Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       21.0Mb
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 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 12.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   8.6Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  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
Imports includes 32 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  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-clang/uuid.Rcheck/00install.out’ for details.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.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.
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:
    extdata   9.1Mb
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespaces in Imports field not imported from:
  ‘rstudioapi’ ‘testthat’
  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.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘saemix’
  All declared Imports should be used.
installed size is  6.0Mb
  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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R   2.5Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Namespaces in Imports field not imported from:
  ‘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.
installed size is 48.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  47.5Mb
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘plyr’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
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
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.
Namespace in Imports field not imported from: ‘ingredients’
  All declared Imports should be used.
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  43.4Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
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.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.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.
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 57.7Mb
  sub-directories of 1Mb or more:
    libs  56.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘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.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.4Mb
Namespaces in Imports field not imported from:
  ‘raster’ ‘reshape2’
  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 ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Matrix’ ‘zoo’
  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 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘later’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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.

Requires orphaned package: ‘gplots’
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  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
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.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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   8.6Mb
possible bashism in configure line 49 (test -a/-o):
  if test ${java_version_maj} -ge 5 || \
      test ${java_version_maj} -eq 1 -a ${java_version_min} -ge 5;
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
Package suggested but not available for checking: ‘ROTS’
Packages unavailable to check Rd xrefs: ‘cleaver’, ‘ROTS’
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    help   1.6Mb
    libs   6.3Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Running ‘testthat.R’ [28s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: opfw - coverage  (@test_opwf.R#69)  ─────────────────────────────
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
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 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
possible bashism in configure line 31 ($(OS|MACH)TYPE):
      if echo $OSTYPE | grep -q '^darwin1[567]'; then
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggdendro’
  All declared Imports should be used.
File ‘xseq/libs/xseq.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:
    include   3.5Mb
    libs      1.7Mb
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.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
Running examples in ‘YPmodel-Ex.R’ failed
The error most likely occurred in:

> ### Name: YPmodel-package
> ### Title: The short-term and long-term hazard ratio model for survival
> ###   data
> ### Aliases: YPmodel-package
> ### Keywords: Survival analysis
> 
> ### ** Examples
> 
> 	library(YPmodel)
> 	data(gastric)
> 	YPmodel(gastric, repNum=100)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
YPmodel
 --- call from context --- 
fun.flipud(s1)
 --- call from argument --- 
if (class(data) != "matrix") {
    data <- matrix(data, nrow = length(data), ncol = 1)
}
 --- R stacktrace ---
where 1: fun.flipud(s1)
where 2: fun.cumsum(fun.flipud(s1))
where 3: fun.flipud(fun.cumsum(fun.flipud(s1)))
where 4: fun.adlgrk(beta, r, Data)
where 5: YPmodel.adlgrk(data = data, Estimate = Estimate)
where 6: YPmodel.default(gastric, repNum = 100)
where 7: YPmodel(gastric, repNum = 100)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data) 
{
    if (class(data) != "matrix") {
        data <- matrix(data, nrow = length(data), ncol = 1)
    }
    size <- dim(data)
    Output <- data
    for (j in 1:size[2]) {
        for (i in 1:size[1]) {
            Output[i, j] <- data[size[1] + 1 - i, j]
        }
    }
    return(Output)
}
<bytecode: 0x1189c38>
<environment: namespace:YPmodel>
 --- function search by body ---
Function fun.flipud in namespace YPmodel has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(data) != "matrix") { : the condition has length > 1
Calls: YPmodel ... fun.adlgrk -> fun.flipud -> fun.cumsum -> fun.flipud
Execution halted
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    libs  38.1Mb
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mzR’
Running examples in ‘bestglm-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneSDRule
> ### Title: Utility function. Implements the 1-sd rule.
> ### Aliases: oneSDRule
> 
> ### ** Examples
> 
> CV<-c(1.4637799,0.7036285,0.6242480,0.6069406,0.6006877,0.6005472,0.5707958,
+       0.5907897,0.5895489)
> CVsd<-c(0.24878992,0.14160499,0.08714908,0.11376041,0.08522291,
+  0.11897327,0.07960879,0.09235052,0.12860983)
> CVout <- matrix(c(CV,CVsd), ncol=2)
> oneSDRule(CVout)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
bestglm
 --- call from context --- 
oneSDRule(CVout)
 --- call from argument --- 
if (class(CVout) == "train") {
    ans <- CVout
    CVout <- with(ans$results, cbind(RMSE, RMSESD))
}
 --- R stacktrace ---
where 1: oneSDRule(CVout)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (CVout) 
{
    stopifnot(is.matrix(CVout) || is.data.frame(CVout) || class(CVout) == 
        "train")
    if (class(CVout) == "train") {
        ans <- CVout
        CVout <- with(ans$results, cbind(RMSE, RMSESD))
    }
    cverrs <- CVout[, 1]
    indMin <- which.min(cverrs)
    fmin <- CVout[indMin, 2]
    cutOff <- fmin + cverrs[indMin]
    min(which(cverrs < cutOff))
}
<bytecode: 0xb7fcd80>
<environment: namespace:bestglm>
 --- function search by body ---
Function oneSDRule in namespace bestglm has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(CVout) == "train") { : the condition has length > 1
Calls: oneSDRule
Execution halted
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Cairo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:207:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:211:34: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:218:45: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:221:65: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:222:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:225:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:236:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:237:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  rcatnet.cpp:368:104: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/catnet.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/circglmbayes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/clpAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/clv.Rcheck/00install.out’ for details.
Running examples in ‘corclass-Ex.R’ failed
The error most likely occurred in:

> ### Name: cca
> ### Title: Main function for CCA.
> ### Aliases: cca
> 
> ### ** Examples
> 
>     data(cca.example)
>     res1 <- cca(cca.example) # with igraph 0.7, this should find 3 classes of sizes 218 391 144.  
Filtering out correlations for which Pr(|r| != 0) >  0.01 
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
corclass
 --- call from context --- 
.separate(attr(cormat, "dtf"), comm$membership)
 --- call from argument --- 
if (class(dtf) == "matrix") {
    rownames(dtf) <- NULL
    dtf <- data.frame(dtf)
}
 --- R stacktrace ---
where 1: .separate(attr(cormat, "dtf"), comm$membership)
where 2: cca(cca.example)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (dtf, membership) 
{
    ids <- sort(unique(membership))
    modules <- list()
    if (class(dtf) == "matrix") {
        rownames(dtf) <- NULL
        dtf <- data.frame(dtf)
    }
    for (i in 1:length(ids)) {
        curmod <- list()
        class(curmod) <- "cca.module"
        curmod$dtf <- dtf[membership == ids[i], ]
        curmod$cormat <- cor(curmod$dtf)
        curmod$degenerate <- any(is.na(curmod$cormat))
        modules[[i]] <- curmod
    }
    return(modules)
}
<bytecode: 0x2b448b8>
<environment: namespace:corclass>
 --- function search by body ---
Function .separate in namespace corclass has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(dtf) == "matrix") { : the condition has length > 1
Calls: cca -> .separate
Execution halted
Found the following significant warnings:
  DTDataFile.cpp:145:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DataGraph.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/datautils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DEploid/vcfReader.cpp:57:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DEploid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:70:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:72:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:74:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:77:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  GetData.c:79:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:210:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:212:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:214:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:217:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:219:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:222:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:224:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  SimulDiv.c:227:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  shpopen.c:1769:22: warning: ‘. Probably broken SHP file’ directive output may be truncated writing 26 bytes into a region of size between 25 and 48 [-Wformat-truncation=]
See ‘/data/gannet/ripley/R/packages/tests-devel/dggridR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/DistributionOptimization.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/dpglasso.Rcheck/00install.out’ for details.
Running examples in ‘drsmooth-Ex.R’ failed
The error most likely occurred in:

> ### Name: noel
> ### Title: No/Lowest Observed Effect Levels
> ### Aliases: noel
> 
> ### ** Examples
> 
> # Prints all available tests of no/lowest observed effect levels at default alpha=.05:
> data(DRdata)
> noel("dose", "MF_Log", data=DRdata)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
drsmooth
 --- call from context --- 
withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
 --- call from argument --- 
if (class(result[[k]]) == "matrix") {
    drsmooth.print(result[[k]])
} else {
    print(result[[k]])
}
 --- R stacktrace ---
where 1: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
where 2: suppressWarnings(for (k in 1:length(result)) {
    if (class(result[[k]]) == "matrix") {
        drsmooth.print(result[[k]])
    }
    else {
        print(result[[k]])
    }
})
where 3: noel("dose", "MF_Log", data = DRdata)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (expr, ...) 
{
    handlers <- list(...)
    classes <- names(handlers)
    parentenv <- parent.frame()
    if (length(classes) != length(handlers)) 
        stop("bad handler specification")
    .Internal(.addCondHands(classes, handlers, parentenv, NULL, 
        TRUE))
    expr
}
<bytecode: 0x292cc30>
<environment: namespace:base>
 --- function search by body ---
Function withCallingHandlers in namespace base has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(result[[k]]) == "matrix") { : 
  the condition has length > 1
Calls: noel
Execution halted
Found the following significant warnings:
  fintegrate.c:350:5: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  gibbsEM.c:417:9: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/eco.Rcheck/00install.out’ for details.
Found the following significant warnings:
  eiutil.c:132:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/eiPack.Rcheck/00install.out’ for details.
Running examples in ‘enaR-Ex.R’ failed
The error most likely occurred in:

> ### Name: enaAll
> ### Title: Conduct All Major ENA
> ### Aliases: enaAll
> 
> ### ** Examples
> 
> 
> 
> 
> data(troModels)
> output = enaAll(troModels[[6]])
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
enaR
 --- call from context --- 
structure.statistics(A)
 --- call from argument --- 
if (class(A) != "matrix") {
    warning("A is not a matrix class object")
}
 --- R stacktrace ---
where 1: structure.statistics(A)
where 2: enaStructure(x)
where 3: enaAll(troModels[[6]])

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (A = "adjacency matrix") 
{
    if (class(A) != "matrix") {
        warning("A is not a matrix class object")
    }
    n <- dim(A)[1]
    L <- sum(A)
    C <- L/n^2
    LD <- L/n
    e <- eigen(A)$values
    aer <- round(abs(e), digits = 7)
    mlam1A <- length(which(aer == aer[1]))
    ppr <- sum(mExp(A, 200))/sum(mExp(A, 199))
    lam1A <- abs(e[1])
    d <- abs(lam1A - LD)
    if ((n - mlam1A) > 0) {
        lam2A <- abs(e[(1 + mlam1A)])
        rho <- lam1A/abs(lam2A)
        R <- abs(e[n]) - abs(e[n - 1])/(abs(e[n - 1]) - abs(e[1]))
    }
    else {
        lam2A <- NA
        rho <- NA
        R <- NA
    }
    sp1 <- as.vector(scc(A)$sp)
    no.scc <- sp1[1]
    no.scc.big <- sp1[2]
    pscc <- sp1[3]
    sp <- cbind(n, L, C, LD, ppr, lam1A, mlam1A, rho, R, d, no.scc, 
        no.scc.big, pscc)
    return(sp)
}
<bytecode: 0x7bfbc30>
<environment: namespace:enaR>
 --- function search by body ---
Function structure.statistics in namespace enaR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(A) != "matrix") { : the condition has length > 1
Calls: enaAll -> enaStructure -> structure.statistics
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/fftw.Rcheck/00install.out’ for details.
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/forestFloor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/freeknotsplines.Rcheck/00install.out’ for details.
Running examples in ‘freestats-Ex.R’ failed
The error most likely occurred in:

> ### Name: adaBoost
> ### Title: Adaboost algorithm
> ### Aliases: adaBoost
> 
> ### ** Examples
> 
> set.seed(1024)
> z <- runif(n=5)
> mydata <- fakedata(w=z,n=100)
> X<- mydata$S[,1:4]
> y <- mydata$y
> res <- adaBoost(dat.train=X,y.train=y,B=3)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
freestats
 --- call from context --- 
train(dat.train, w, y.train, ...)
 --- call from argument --- 
if (class(w) != "matrix") {
    w <- as.matrix(w)
}
 --- R stacktrace ---
where 1: train(dat.train, w, y.train, ...)
where 2: adaBoost(dat.train = X, y.train = y, B = 3)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (X, w, y) 
{
    if (class(w) != "matrix") {
        w <- as.matrix(w)
    }
    theta <- vector()
    best.cost <- vector()
    Compare <- 10
    for (d in 1:dim(X)[2]) {
        if (!is.factor(X[, d])) {
            for (n in 1:dim(X)[1]) {
                yhat <- 2 * (X[, d] > X[n, d]) - 1
                cost.temp <- t(w) %*% (y != yhat)/sum(w)
                if (cost.temp < Compare) {
                  Compare <- cost.temp
                  best.theta <- X[n, d]
                  best.j <- d
                  best.n <- n
                }
            }
        }
        else stop("only for numeric input now!")
    }
    res <- list(j = best.j, theta = best.theta, m = 1)
    class(res) <- "ds"
    return(res)
}
<bytecode: 0x3422d08>
<environment: namespace:freestats>
 --- function search by body ---
Function decisionStump in namespace freestats has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(w) != "matrix") { : the condition has length > 1
Calls: adaBoost -> train
Execution halted
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/FunctionalNetworks.Rcheck/00install.out’ for details.
Running examples in ‘GENLIB-Ex.R’ failed
The error most likely occurred in:

> ### Name: gen.phiMean
> ### Title: Average kinship
> ### Aliases: gen.phiMean
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(geneaJi) 
> genJi<-gen.genealogy(geneaJi) 
> kinship<-gen.phi(genJi)
> gen.phiMean(kinship)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
GENLIB
 --- call from context --- 
gen.phiMean(kinship)
 --- call from argument --- 
if (class(phiMatrix) == "matrix") mean(phiMatrix[phiMatrix < 
    0.5]) else GLapplyPhi(phiMatrix, function(x) mean(x[x < 0.5]), 
    named = named)
 --- R stacktrace ---
where 1: gen.phiMean(kinship)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (phiMatrix) 
{
    retour = gen.detectionErreur(matricephi = phiMatrix, named = T, 
        check = c(28, 10))
    if (retour$erreur == T) 
        stop(retour$messageErreur)
    phiMatrix = retour$matricephi
    named = retour$named
    if (class(phiMatrix) == "matrix") 
        mean(phiMatrix[phiMatrix < 0.5])
    else GLapplyPhi(phiMatrix, function(x) mean(x[x < 0.5]), 
        named = named)
}
<bytecode: 0xb349590>
<environment: namespace:GENLIB>
 --- function search by body ---
Function gen.phiMean in namespace GENLIB has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(phiMatrix) == "matrix") mean(phiMatrix[phiMatrix <  : 
  the condition has length > 1
Calls: gen.phiMean
Execution halted
Found the following significant warnings:
  runMCMCfunc.cpp:40:40: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:43: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:45: warning: left operand of comma operator has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/geoCount.Rcheck/00install.out’ for details.
Running examples in ‘geodetector-Ex.R’ failed
The error most likely occurred in:

> ### Name: interaction_detector
> ### Title: interaction detector
> ### Aliases: interaction_detector
> ### Keywords: detector interaction
> 
> ### ** Examples
> 
> data(CollectData)
> interaction_detector("incidence",c("soiltype","watershed"),CollectData)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
geodetector
 --- call from context --- 
reshapeMatrix_numeric(Intr_Result_q)
 --- call from argument --- 
if (class(dataset) == "character") dataset = t(as.matrix(dataset))
 --- R stacktrace ---
where 1: reshapeMatrix_numeric(Intr_Result_q)
where 2: interaction_detector("incidence", c("soiltype", "watershed"), 
    CollectData)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (dataset) 
{
    if (class(dataset) == "character") 
        dataset = t(as.matrix(dataset))
    fldName1 <- as.vector(dataset[, 1])
    fldName2 <- as.vector(dataset[, 2])
    fldName <- unique(c(fldName1, fldName2))
    lenFld <- length(fldName)
    CreatMat <- matrix(nrow = lenFld, ncol = lenFld, dimnames = list(fldName, 
        fldName))
    lenDt <- nrow(dataset)
    for (i in 1:lenDt) {
        fld1 <- fldName1[i]
        fld2 <- fldName2[i]
        CreatMat[fld1, fld2] <- as.vector(dataset[i, 3])
        CreatMat[fld2, fld1] <- as.vector(dataset[i, 3])
    }
    T_CreatMat <- as.data.frame(CreatMat)
    return(T_CreatMat)
}
<bytecode: 0x5b60f60>
<environment: namespace:geodetector>
 --- function search by body ---
Function reshapeMatrix_numeric in namespace geodetector has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(dataset) == "character") dataset = t(as.matrix(dataset)) : 
  the condition has length > 1
Calls: interaction_detector -> reshapeMatrix_numeric
Execution halted
Running examples in ‘geomnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: fortify.adjmat
> ### Title: Function for converting a network adjacency matrix into the
> ###   correct format for use with geomnet
> ### Aliases: fortify.adjmat
> 
> ### ** Examples
> 
> data(emon, package = "network")
> adjmat <- as.adjmat(network::as.matrix.network.adjacency(emon$MtSi))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
geomnet
 --- call from context --- 
as.adjmat(network::as.matrix.network.adjacency(emon$MtSi))
 --- call from argument --- 
if (class(dat) != "matrix") {
    stop("as.adjmat requires a matrix object")
}
 --- R stacktrace ---
where 1: as.adjmat(network::as.matrix.network.adjacency(emon$MtSi))

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (dat) 
{
    if (class(dat) != "matrix") {
        stop("as.adjmat requires a matrix object")
    }
    if (nrow(dat) != ncol(dat)) {
        stop("dat must be a square matrix")
    }
    if (sum(rownames(dat) != colnames(dat)) > 0) {
        stop("row and column names of dat must match")
    }
    class(dat) <- c("adjmat", "matrix")
    return(dat)
}
<bytecode: 0x46bea70>
<environment: namespace:geomnet>
 --- function search by body ---
Function as.adjmat in namespace geomnet has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(dat) != "matrix") { : the condition has length > 1
Calls: as.adjmat
Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/gglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Converter.cpp:154:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Converter.cpp:157:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:387:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:388:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:193:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:197:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:230:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Sequence.cpp:292:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/gkmSVM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/glpkAPI.Rcheck/00install.out’ for details.
Running examples in ‘gofMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: KS_D
> ### Title: KS_D
> ### Aliases: KS_D
> 
> ### ** Examples
> 
> KS_D(c(1,2,3,4,5),c(1,2,3,4,4))
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
gofMC
 --- call from context --- 
fitmetric_check(x, y)
 --- call from argument --- 
if (class(x) == "matrix" & class(y) == "matrix" & dim(x)[[1]] == 
    dim(y)[[1]] & dim(x)[[2]] == dim(y)[[2]]) {
    N = dim(x)[[1]]
    dof = dim(x)[[2]]
}
 --- R stacktrace ---
where 1: fitmetric_check(x, y)
where 2: KS_D(c(1, 2, 3, 4, 5), c(1, 2, 3, 4, 4))

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x, y) 
{
    gclasses <- c("numeric", "integer")
    if (class(x) %in% gclasses & class(y) %in% gclasses & length(x) == 
        length(y)) {
        x <- matrix(x, nrow = 1)
        y <- matrix(y, nrow = 1)
    }
    else if (class(x) == "matrix" & class(y) == "matrix") {
    }
    else {
        stop("x & y classes or lengths different")
    }
    if (ncol(x) == 1 | ncol(y) == 1) {
        stop("can not compute fit with only one value")
    }
    if (class(x) == "matrix" & class(y) == "matrix" & dim(x)[[1]] == 
        dim(y)[[1]] & dim(x)[[2]] == dim(y)[[2]]) {
        N = dim(x)[[1]]
        dof = dim(x)[[2]]
    }
    mlist <- list(x, y, N, dof)
    return(mlist)
}
<bytecode: 0x3a64a38>
<environment: namespace:gofMC>
 --- function search by body ---
Function fitmetric_check in namespace gofMC has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "matrix" & class(y) == "matrix" & dim(x)[[1]] ==  : 
  the condition has length > 1
Calls: KS_D -> fitmetric_check
Execution halted
Found the following significant warnings:
  gpc.c:1036:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1043:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1046:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1053:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/gpclib.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  gener.c:39:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  gener.c:39:26: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hier.part.Rcheck/00install.out’ for details.
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.
Running examples in ‘hybridHclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: get.distances
> ### Title: Extract Distances From Mutual Cluster
> ### Aliases: get.distances
> ### Keywords: cluster
> 
> ### ** Examples
> 
> x <- cbind(c(-1.4806,1.5772,-0.9567,-0.92,-1.9976,-0.2723,-0.3153),
+            c(-0.6283,-0.1065,0.428,-0.7777,-1.2939,-0.7796,0.012))
> mc1 <- mutualCluster(x)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
hybridHclust
 --- call from context --- 
setmc(d[[1]], dmat)
 --- call from argument --- 
if (class(dmat) == "dist") dmat <- as.matrix(dmat)
 --- R stacktrace ---
where 1: setmc(d[[1]], dmat)
where 2: setmc(setobs(as.dendrogram(h)), dmat)
where 3: getmc(h, distances, plot)
where 4: mutualCluster(x)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (d, dmat) 
{
    if (class(dmat) == "dist") 
        dmat <- as.matrix(dmat)
    if (attr(d, "members") > 1) {
        d[[1]] <- setmc(d[[1]], dmat)
        d[[2]] <- setmc(d[[2]], dmat)
        obs <- attr(d, "obs")
        if ((length(obs) < nrow(dmat)) && (max(dmat[obs, obs]) < 
            min(dmat[obs, -obs]))) 
            attr(d, "edgetext") <- " "
    }
    return(d)
}
<bytecode: 0x2cc2268>
<environment: namespace:hybridHclust>
 --- function search by body ---
Function setmc in namespace hybridHclust has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(dmat) == "dist") dmat <- as.matrix(dmat) : 
  the condition has length > 1
Calls: mutualCluster -> getmc -> setmc -> setmc
Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/icd.Rcheck/00install.out’ for details.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/JavaGD.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  matrix.c:827:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:833:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:843:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:979:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1007:1: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1051:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1101:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
  matrix.c:1155:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/knncat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: 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-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: 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-4.0/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: 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.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ManifoldOptim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See ‘/data/gannet/ripley/R/packages/tests-devel/MatrixModels.Rcheck/00install.out’ for details.
Running examples in ‘memnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: alc
> ### Title: Average local clustering (alc) coefficient
> ### Aliases: alc
> 
> ### ** Examples
> 
> 
> # get fluency data
> data(animal_fluency)
> 
> # edge lists of fluency graphs
> edge_list = threshold_graph(animal_fluency)
> 
> # get adjacency matrices
> adj = edg_to_adj(edge_list)
> 
> # get local average clustering coefficient
> alc(adj)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
memnet
 --- call from context --- 
alc(adj)
 --- call from argument --- 
if (class(adj) != "igraph") {
    g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
    if (!is.null(weights)) 
        igraph::E(g)$weight = weights
} else {
    g = adj
}
 --- R stacktrace ---
where 1: alc(adj)

 --- value of length: 2 type: logical ---
[1] TRUE TRUE
 --- function from context --- 
function (adj, types = "uncorrected", weights = NULL, mode = "undirected") 
{
    if (class(adj) != "igraph") {
        g = igraph::graph_from_adjacency_matrix(adj, mode = mode)
        if (!is.null(weights)) 
            igraph::E(g)$weight = weights
    }
    else {
        g = adj
    }
    res = c()
    cc = igraph::transitivity(g, type = "localaverage")
    for (type in types) {
        if (type == "uncorrected") {
            res = c(res, cc)
            names(res)[length(res)] = "cc"
        }
        else if (type == "corrected") {
            nv = igraph::vcount(g)
            ne = igraph::ecount(g)
            k = ne/nv
            res = c(res, cc/(k/nv))
            names(res)[length(res)] = "cc_c"
        }
    }
    res
}
<bytecode: 0x3851908>
<environment: namespace:memnet>
 --- function search by body ---
Function alc in namespace memnet has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(adj) != "igraph") { : the condition has length > 1
Calls: alc
Execution halted
Found the following significant warnings:
  migrate.c:180:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:187:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:200:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:287:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:313:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:560:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:596:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:604:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/MigClim.Rcheck/00install.out’ for details.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
  'config' variable 'CXXCPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/nloptr.Rcheck/00install.out’ for details.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  rcpp_nativecont.cpp:30:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_nativecont.cpp:34:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segBreedComp.cpp:42:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segBreedComp.cpp:45:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  rcpp_segN.cpp:48:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/optiSel.Rcheck/00install.out’ for details.
Running examples in ‘PCIT-Ex.R’ failed
The error most likely occurred in:

> ### Name: idxInvert
> ### Title: Invert linear indices from a matrix
> ### Aliases: idxInvert
> 
> ### ** Examples
> 
> 	m <- matrix(1, 5, 5)
> 	diag(m) <- 0
> 	m
     [,1] [,2] [,3] [,4] [,5]
[1,]    0    1    1    1    1
[2,]    1    0    1    1    1
[3,]    1    1    0    1    1
[4,]    1    1    1    0    1
[5,]    1    1    1    1    0
> 	idx <- which(m==0)
> 	idx
[1]  1  7 13 19 25
> 	idxInvert(m, idx)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
PCIT
 --- call from context --- 
idxInvert(m, idx)
 --- call from argument --- 
if (class(m) == "numeric" | class(m) == "integer") {
    nNodes <- m
} else {
    nNodes <- try(nrow(m), silent = TRUE)
    if (class(nNodes) == "try-error" | is.null(nNodes)) {
        cat("ERROR: argument 'm' must be a numeric OR an object on which nrow() can be performed.\n\n", 
            geterrmessage())
        return(FALSE)
    }
}
 --- R stacktrace ---
where 1: idxInvert(m, idx)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (m, idx) 
{
    if (class(m) == "numeric" | class(m) == "integer") {
        nNodes <- m
    }
    else {
        nNodes <- try(nrow(m), silent = TRUE)
        if (class(nNodes) == "try-error" | is.null(nNodes)) {
            cat("ERROR: argument 'm' must be a numeric OR an object on which nrow() can be performed.\n\n", 
                geterrmessage())
            return(FALSE)
        }
    }
    return(setdiff(1:(nNodes^2), idx))
}
<bytecode: 0x41b64f8>
<environment: namespace:PCIT>
 --- function search by body ---
Function idxInvert in namespace PCIT has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(m) == "numeric" | class(m) == "integer") { : 
  the condition has length > 1
Calls: idxInvert
Execution halted
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/permDep.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Serialize.h:64:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  Serialize.h:66:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  Serialize.h:68:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  mbart.cpp:512:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
  mbart.cpp:513:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/pgbart.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [98s/116s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PlackettLuce)
  > 
  > test_check("PlackettLuce")
  ── 1. Error: (unknown) (@test-log-likelihood.R#81)  ────────────────────────────
  The package Matrix.utils is needed for this function to work. Please install it.
  Backtrace:
   1. BradleyTerryScalable::btdata(as.data.frame(cbind(M, 1)))
   2. BradleyTerryScalable:::pairs_to_matrix(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 168 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-log-likelihood.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [157s/168s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  ── 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ─────────
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1390 | SKIPPED: 43 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/proj4.Rcheck/00install.out’ for details.
Found the following significant warnings:
  pts2polys.cpp:1560:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/pts2polys.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:103:12: warning: ignoring return value of ‘ssize_t write(int, const void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
  /data/gannet/ripley/R/packages/tests-devel/qtbase/src/EventLoop.cpp:92:7: warning: ignoring return value of ‘ssize_t read(int, void*, size_t)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/qtbase.Rcheck/00install.out’ for details.
Found the following file(s) containing GNU extensions:
  src-build/Makefile
  tools/kdebindings-build/Makefile
  tools/kdebindings-build/generator/Makefile
  tools/kdebindings-build/generator/generators/Makefile
  tools/kdebindings-build/generator/generators/dump/Makefile
  tools/kdebindings-build/generator/generators/smoke/Makefile
  tools/kdebindings-build/generator/parser/Makefile
  tools/kdebindings-build/smoke/Makefile
  tools/kdebindings-build/smoke/qt/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.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.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.
Found the following significant warnings:
  Routines/xml_file_read.cc:154:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  Routines/xml_file_read.cc:243:9: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/R2GUESS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/R4dfp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘scran’
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RArcInfo.Rcheck/00install.out’ for details.
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 significant warnings:
  'config' variable 'CPP' is deprecated
  Rreadsdpa.c:496:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:504:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:528:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:540:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:549:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:554:55: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:560:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:602:54: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:607:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  Rreadsdpa.c:1028:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  dsdpsetoptions.c:161:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/re2r.Rcheck/00install.out’ for details.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(remotes)
  > 
  > test_check("remotes")
  
  
  ── 1. Failure: safe_build_package fails appropriately with pkgbuild (@test-insta
  `safe_build_package(...)` threw an error with unexpected message.
  Expected match: "System command error"
  Actual message: "System command 'R' failed, exit status: 1, stdout + stderr:\nE> * checking for file ‘/data/gannet/ripley/R/packages/tests-devel/remotes.Rcheck/tests/testthat/invalidpkg/DESCRIPTION’ ... OK\nE> * preparing ‘invalidpkg’:\nE> * checking DESCRIPTION meta-information ... ERROR\nE> Malformed Depends or Suggests or Imports or Enhances field.\nE> Offending entries:\nE>   testthat\nE> foobar\nE> Entries must be names of packages optionally followed by '<=' or '>=',\nE> white space, and a valid version number in parentheses.\nE> \nE> See section 'The DESCRIPTION file' in the 'Writing R Extensions'\nE> manual.\nE> "
  Backtrace:
    1. testthat::expect_error(...)
    6. remotes:::safe_build_package(...)
    7. pkgbuild::build(...)
   10. pkgbuild::rcmd_build_tools(...)
   12. callr::rcmd_safe(...)
   13. callr:::run_r(options)
   15. base::with.default(...)
   16. [ base::eval(...) ] with 1 more call
   22. throw(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 396 | SKIPPED: 78 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: safe_build_package fails appropriately with pkgbuild (@test-install.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
Quitting from lines 273-284 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘UsingrerddapXtracto.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/rgl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'playwith', 'pmg'
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’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.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 significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See ‘/data/gannet/ripley/R/packages/tests-devel/RobExtremes.Rcheck/00install.out’ for details.
Running examples in ‘rotations-Ex.R’ failed
The error most likely occurred in:

> ### Name: Arithmetic
> ### Title: Arithmetic operators on SO(3)
> ### Aliases: "+.Q4" "+.SO3" "-.Q4" "-.SO3" +.Q4 +.SO3 -.Q4 -.SO3 Arithmetic
> 
> ### ** Examples
> 
> U <- c(1, 0, 0)          #Rotate about the x-axis
> R1 <- as.SO3(U, pi/8)    #Rotate pi/8 radians about the x-axis
> R2 <- R1 + R1            #Rotate pi/8 radians about the x-axis twice
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
rotations
 --- call from context --- 
is.SO3(Rs)
 --- call from argument --- 
if (class(x) == "data.frame") R <- data.matrix(R)
 --- R stacktrace ---
where 1: is.SO3(Rs)
where 2: formatSO3(x)
where 3: center.SO3(x, y)
where 4: center(x, y)
where 5: `+.SO3`(R1, R1)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x) 
{
    Rlen <- length(x)
    if (Rlen%%9 != 0) {
        return(FALSE)
    }
    R <- x
    if (class(x) == "data.frame") 
        R <- data.matrix(R)
    R <- matrix(R, ncol = 9)
    apply(R, 1, function(R) {
        R <- matrix(R, 3, 3)
        if (any(is.na(R))) 
            return(FALSE)
        if (abs(det(R) - 1) > 1e-09) 
            return(FALSE)
        return(all(abs(t(R) %*% R - diag(1, 3)) < 1e-04))
    })
}
<bytecode: 0x70678c8>
<environment: namespace:rotations>
 --- function search by body ---
Function is.SO3 in namespace rotations has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "data.frame") R <- data.matrix(R) : 
  the condition has length > 1
Calls: +.SO3 -> center -> center.SO3 -> formatSO3 -> is.SO3
Execution halted
Found the following significant warnings:
  bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rng.cpp:43:22: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/Rsampletrees.Rcheck/00install.out’ for details.
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 significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/Rssa.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘rstanarm’
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:222:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:226:34: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:233:45: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:236:65: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:237:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:240:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:251:63: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  catnet_rexport.cpp:252:36: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  rcatnet_prob.cpp:49:104: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdwd.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'loomR', 'MAST', 'monocle'
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/BH/include/boost/graph/detail/adjacency_list.hpp:2239:43: warning: ‘p.Edge::color’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SimilaR.Rcheck/00install.out’ for details.
Running examples in ‘SimuChemPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: SimuChemPC
> ### Title: SimuChemPC
> ### Aliases: SimuChemPC 'SimuChemPC, character list, character list,
> ###   character list, character list,integer'
> ### Keywords: chemical, potent compounds, constraint global optimization,
> ###   expected potency improvement, gaussian process
> 
> ### ** Examples
> 
> x = as.data.frame(array(1:100, dim=c(20,5)))
> y = as.matrix(as.numeric(array(1:20, dim=c(20,1))))
> SimuChemPC(x, y, "RA", 5)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SimuChemPC
 --- call from context --- 
normalize(yTrain)
 --- call from argument --- 
if (class(x) == "data.frame") {
    sigma = sapply(x_norm, sd)
} else {
    sigma = sd(x_norm)
}
 --- R stacktrace ---
where 1: normalize(yTrain)
where 2: SimuChemPC(x, y, "RA", 5)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x) 
{
    mu = colMeans(x)
    x_norm = sweep(x, length(dim(x)), mu, FUN = "-")
    if (class(x) == "data.frame") {
        sigma = sapply(x_norm, sd)
    }
    else {
        sigma = sd(x_norm)
    }
    sigma[sigma == 0] = 1
    norm = sweep(x_norm, length(dim(x)), sigma, FUN = "/")
    return(list(norm, mu, sigma))
}
<bytecode: 0x42e3c88>
<environment: namespace:SimuChemPC>
 --- function search by body ---
Function normalize in namespace SimuChemPC has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "data.frame") { : the condition has length > 1
Calls: SimuChemPC -> normalize
Execution halted
Running examples in ‘skyscapeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: reduct.compass
> ### Title: Data reduction for compass measurements
> ### Aliases: reduct.compass
> 
> ### ** Examples
> 
> loc <- c(35,-7)
> mag.az <- c(89.5, 105, 109.5)
> data <- reduct.compass(loc, mag.az, "2016/04/02")
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
skyscapeR
 --- call from context --- 
mag.dec(loc, date)
 --- call from argument --- 
if (class(loc) == "skyscapeR.horizon") {
    loc <- loc$georef
}
 --- R stacktrace ---
where 1: mag.dec(loc, date)
where 2: reduct.compass(loc, mag.az, "2016/04/02")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (loc, date) 
{
    if (class(loc) == "skyscapeR.horizon") {
        loc <- loc$georef
    }
    if (is.null(dim(loc))) {
        dim(loc) <- c(1, NROW(loc))
    }
    aux <- oce::magneticField(loc[, 2], loc[, 1], as.POSIXlt(date, 
        format = "%Y/%m/%d"))$declination
    return(aux)
}
<bytecode: 0xa6b6888>
<environment: namespace:skyscapeR>
 --- function search by body ---
Function mag.dec in namespace skyscapeR has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(loc) == "skyscapeR.horizon") { : 
  the condition has length > 1
Calls: reduct.compass -> mag.dec
Execution halted
Found the following significant warnings:
  slfm_MDN.cpp:26:38: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:38: warning: left operand of comma operator has no effect [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/slfm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gpc.c:1039:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1046:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1049:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  gpc.c:1056:7: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/spatialkernel.Rcheck/00install.out’ for details.
Running examples in ‘SpecsVerification-Ex.R’ failed
The error most likely occurred in:

> ### Name: Detrend
> ### Title: Auxiliary function for removing trends and mean from observation
> ###   vector or ensemble matrix.
> ### Aliases: Detrend
> 
> ### ** Examples
> 
>  data(eurotempforecast)
>  Detrend(ens)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
SpecsVerification
 --- call from context --- 
Detrend(ens)
 --- call from argument --- 
if (class(x) == "matrix") {
    xx <- rowMeans(x, na.rm = TRUE)
} else {
    xx <- x
}
 --- R stacktrace ---
where 1: Detrend(ens)

 --- value of length: 2 type: logical ---
[1]  TRUE FALSE
 --- function from context --- 
function (x, demean = TRUE) 
{
    if (class(x) == "matrix") {
        xx <- rowMeans(x, na.rm = TRUE)
    }
    else {
        xx <- x
    }
    N <- length(xx)
    if (N == 1) {
        trnd <- x
    }
    else {
        t <- 1:N
        lmod <- lm(xx ~ t)
        trnd <- drop(cbind(1, t) %*% coef(lmod))
    }
    m <- ifelse(demean, 0, mean(unlist(x), na.rm = TRUE))
    return(x - trnd + m)
}
<bytecode: 0x2b3e790>
<environment: namespace:SpecsVerification>
 --- function search by body ---
Function Detrend in namespace SpecsVerification has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "matrix") { : the condition has length > 1
Calls: Detrend
Execution halted
Running examples in ‘squash-Ex.R’ failed
The error most likely occurred in:

> ### Name: corrogram
> ### Title: Draw a color-coded triangular matrix of pairwise correlations
> ### Aliases: corrogram
> ### Keywords: hplot
> 
> ### ** Examples
>  
>   
>   corrogram(cor(swiss), title = 'Pearson correlation')
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
squash
 --- call from context --- 
distogram(..., map = map)
 --- call from argument --- 
if (class(x) == "dist") x <- as.matrix(x)
 --- R stacktrace ---
where 1: distogram(..., map = map)
where 2: corrogram(cor(swiss), title = "Pearson correlation")

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x, map, n = 10, base = NA, colFn = heat, key = TRUE, 
    title = NA, ...) 
{
    if (class(x) == "dist") 
        x <- as.matrix(x)
    stopifnot(nrow(x) == ncol(x))
    if (missing(map)) {
        map <- makecmap(x, n = n, base = base, colFn = colFn)
    }
    trianglegram(cmap(x, map = map), ...)
    if (key) 
        hkey(map = map, title = title)
    invisible(map)
}
<bytecode: 0x3d0d900>
<environment: namespace:squash>
 --- function search by body ---
Function distogram in namespace squash has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(x) == "dist") x <- as.matrix(x) : 
  the condition has length > 1
Calls: corrogram -> distogram
Execution halted
Found the following significant warnings:
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  init.c:63:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:64:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:95:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:100:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:132:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:142:7: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:153:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
  init.c:156:3: warning: ignoring return value of ‘scanf’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/stepwise.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/SuperGauss.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See ‘/data/gannet/ripley/R/packages/tests-devel/svmadmm.Rcheck/00install.out’ for details.
Running examples in ‘TempleMetrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: Fycondx.DR
> ### Title: Fycondx.DR
> ### Aliases: Fycondx.DR
> 
> ### ** Examples
> 
> data(igm)
> yvals <- seq(quantile(igm$lcfincome,.05,type=1),
+  quantile(igm$lcfincome,.95, type=1), length.out=100)
> dres <- distreg(lcfincome ~ lfincome + HEDUC, igm, yvals)
> xdf <- data.frame(lfincome=10, HEDUC=c("LessHS","HS"))
> d <- Fycondx(dres, yvals, xdf)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
TempleMetrics
 --- call from context --- 
Fycondx.DR(dres, yvals, xdf)
 --- call from argument --- 
if (class(predmat) == "numeric") {
    predmat <- t(predmat)
}
 --- R stacktrace ---
where 1: Fycondx.DR(dres, yvals, xdf)
where 2: Fycondx(dres, yvals, xdf)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (object, yvals, xdf) 
{
    drobj <- object
    yvals <- drobj$yvals
    glmlist <- drobj$glmlist
    predmat <- sapply(glmlist, function(g) {
        predict(g, newdata = xdf, type = "response")
    })
    if (class(predmat) == "numeric") {
        predmat <- t(predmat)
    }
    out <- lapply(1:nrow(predmat), function(i) {
        makeDist(yvals, predmat[i, ], rearrange = TRUE)
    })
    out
}
<bytecode: 0x111ef08>
<environment: namespace:TempleMetrics>
 --- function search by body ---
Function Fycondx.DR in namespace TempleMetrics has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(predmat) == "numeric") { : 
  the condition has length > 1
Calls: Fycondx -> Fycondx.DR
Execution halted
Found the following significant warnings:
  /data/gannet/ripley/R/test-4.0/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-4.0/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/text2vec.Rcheck/00install.out’ for details.
Running examples in ‘tinter-Ex.R’ failed
The error most likely occurred in:

> ### Name: darken
> ### Title: Darken colour.
> ### Aliases: darken
> 
> ### ** Examples
> 
> darken(tinter("blue"), 0.2)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
tinter
 --- call from context --- 
check_colour(x)
 --- call from argument --- 
if (class(res) == "try-error") stop(x, " is not a valid color", 
    call. = FALSE)
 --- R stacktrace ---
where 1: check_colour(x)
where 2: tinter("blue")
where 3: lapply(x, check_colour)
where 4: darken(tinter("blue"), 0.2)

 --- value of length: 2 type: logical ---
[1] FALSE FALSE
 --- function from context --- 
function (x) 
{
    res <- try(grDevices::col2rgb(x), silent = TRUE)
    if (class(res) == "try-error") 
        stop(x, " is not a valid color", call. = FALSE)
}
<bytecode: 0x1673480>
<environment: namespace:tinter>
 --- function search by body ---
Function check_colour in namespace tinter has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(res) == "try-error") stop(x, " is not a valid color",  : 
  the condition has length > 1
Calls: darken -> lapply -> tinter -> check_colour
Execution halted
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.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.
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 significant warnings:
  /usr/include/bits/string_fortified.h:136:10: warning: ‘__builtin___strncat_chk’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  'config' variable 'CPP' is deprecated
See ‘/data/gannet/ripley/R/packages/tests-devel/uuid.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  vic/drivers/shared_all/src/compress_files.c:49:5: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/forcing_utils.c:140:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/forcing_utils.c:161:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:43:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:51:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/get_parameters.c:540:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/input_tools.c:77:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/input_tools.c:101:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/open_file.c:89:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
  vic/drivers/shared_all/src/open_file.c:98:17: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/VICmodel.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 significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
  assp/labelobj.c:165:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
See ‘/data/gannet/ripley/R/packages/tests-devel/wrassp.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [35s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: opfw - coverage  (@test_opwf.R#69)  ─────────────────────────────
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Running examples in ‘YPmodel-Ex.R’ failed
The error most likely occurred in:

> ### Name: YPmodel-package
> ### Title: The short-term and long-term hazard ratio model for survival
> ###   data
> ### Aliases: YPmodel-package
> ### Keywords: Survival analysis
> 
> ### ** Examples
> 
> 	library(YPmodel)
> 	data(gastric)
> 	YPmodel(gastric, repNum=100)
 ----------- FAILURE REPORT -------------- 
 --- failure: the condition has length > 1 ---
 --- srcref --- 
: 
 --- package (from environment) --- 
YPmodel
 --- call from context --- 
fun.flipud(s1)
 --- call from argument --- 
if (class(data) != "matrix") {
    data <- matrix(data, nrow = length(data), ncol = 1)
}
 --- R stacktrace ---
where 1: fun.flipud(s1)
where 2: fun.cumsum(fun.flipud(s1))
where 3: fun.flipud(fun.cumsum(fun.flipud(s1)))
where 4: fun.adlgrk(beta, r, Data)
where 5: YPmodel.adlgrk(data = data, Estimate = Estimate)
where 6: YPmodel.default(gastric, repNum = 100)
where 7: YPmodel(gastric, repNum = 100)

 --- value of length: 2 type: logical ---
[1] FALSE  TRUE
 --- function from context --- 
function (data) 
{
    if (class(data) != "matrix") {
        data <- matrix(data, nrow = length(data), ncol = 1)
    }
    size <- dim(data)
    Output <- data
    for (j in 1:size[2]) {
        for (i in 1:size[1]) {
            Output[i, j] <- data[size[1] + 1 - i, j]
        }
    }
    return(Output)
}
<bytecode: 0x17898a0>
<environment: namespace:YPmodel>
 --- function search by body ---
Function fun.flipud in namespace YPmodel has this body.
 ----------- END OF FAILURE REPORT -------------- 
Error in if (class(data) != "matrix") { : the condition has length > 1
Calls: YPmodel ... fun.adlgrk -> fun.flipud -> fun.cumsum -> fun.flipud
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    R  14.6Mb
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    data  20.8Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(AGread)
  package 'AGread' was built under R version 3.5.0
  > 
  > test_check("AGread")
  -- 1. Failure: gt3x file reading and operations are consistent (@test_gt3x.R#17)
  test$RAW has changed from known value recorded in 'read_3x_raw.rds'.
  Component "Accelerometer_X": Mean relative difference: 0.004810997
  Component "Accelerometer_Y": Mean relative difference: 0.001231321
  Component "Accelerometer_Z": Mean relative difference: 0.003440402
  
  -- 2. Failure: gt3x file reading and operations are consistent (@test_gt3x.R#30)
  collapse_gt3x(test$RAW)[, -2] has changed from known value recorded in 'read_3x_raw_1s.rds'.
  Component "ENMO": Mean relative difference: 0.0001720309
  
  == testthat results  ===========================================================
  [ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: gt3x file reading and operations are consistent (@test_gt3x.R#17) 
  2. Failure: gt3x file reading and operations are consistent (@test_gt3x.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  ADAPTgdwm.c:136:13: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/AMORE.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.2Mb
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  6.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   1.8Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ape.Rcheck/00install.out' for details.
Running examples in 'archivist-Ex.R' failed
The error most likely occurred in:

> ### Name: aread
> ### Title: Read Artifacts Given as md5hashes from the Repository
> ### Aliases: aread
> 
> ### ** Examples
> 
> # read the object from local directory
> setLocalRepo(system.file("graphGallery", package = "archivist"))
> pl <- aread("7f3453331910e3f321ef97d87adb5bad")
> # To plot it remember to have ggplot2 in version 2.1.0
> # as this is stated in asession("7f3453331910e3f321ef97d87adb5bad") .
> # The state of R libraries can be restored to the same state in
> # which 7f3453331910e3f321ef97d87adb5bad was created with the restoreLibs function.
> 
> # read the object from Remote
> pl <- aread("pbiecek/graphGallery/7f3453331910e3f321ef97d87adb5bad")
Error in function (type, msg, asError = TRUE)  : 
  Could not resolve host: raw.githubusercontent.com
Calls: aread ... getBinaryURL -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  12.9Mb
Error(s) in re-building vignettes:
--- re-building 'a_intro_attempt.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/ColinFay/attempt/master/README-fig/attempt_hex_200.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/ColinFay/attempt/master/README-fig/attempt_hex_200.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'a_intro_attempt.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'a_intro_attempt.Rmd'

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Data_Analysis_with_augmentedRCBD.Rmd' using rmarkdown_notangle
trying URL 'https://www.r-project.org/logo/Rlogo.png'
Content type 'image/png' length 48148 bytes (47 KB)
==================================================
downloaded 47 KB

trying URL 'https://raw.githubusercontent.com/aravind-j/augmentedRCBD/master/vignettes/rbase.png'
Quitting from lines 129-137 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/aravind-j/augmentedRCBD/master/vignettes/rbase.png'
--- failed re-building 'Data_Analysis_with_augmentedRCBD.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'rPython'
Error(s) in re-building vignettes:
--- re-building 'AutoDeskR.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://github.com/paulgovan/AutoDeskR/blob/master/inst/images/basicSample.png?raw=true
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/paulgovan/AutoDeskR/blob/master/inst/images/basicSample.png"
  queryString          = "?raw=true"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'AutoDeskR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'AutoDeskR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.8Mb
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) (2020-01-28 r77738) -- "Unsuffered Consequences"
Copyright (C) 2020 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  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   1.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Error(s) in re-building vignettes:
--- re-building 'Using-baRcodeR.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/yihanwu/baRcodeR/master/man/figures/Flowchart.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/yihanwu/baRcodeR/master/man/figures/Flowchart.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Using-baRcodeR.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Using-baRcodeR.Rmd'

--- re-building 'use-addin.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/yihanwu/baRcodeR/master/man/figures/Flowchart.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/yihanwu/baRcodeR/master/man/figures/Flowchart.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'use-addin.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'use-addin.Rmd'

SUMMARY: processing the following files failed:
  'Using-baRcodeR.Rmd' 'use-addin.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.0Mb
Running examples in 'baseballDBR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_bbdb
> ### Title: Get an up to date copy of the Baseball Databank.
> ### Aliases: get_bbdb
> ### Keywords: data database, frame
> 
> ### ** Examples
> 
> 
> get_bbdb(table = "Batting")
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(file, "rt") : cannot open the connection
Calls: get_bbdb -> list2env -> lapply -> FUN -> read.table -> file
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#21)  ------------------------------
  urlExists("https://raw.githubusercontent.com/chadwickbureau/baseballdatabank/master/core/AllstarFull.csv") isn't true.
  
  -- 2. Failure: (unknown) (@test-check_urls.R#23)  ------------------------------
  urlExists("https://raw.githubusercontent.com/keberwein/baseballdatabank/master/core/AllstarFull.csv") isn't true.
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: (unknown) (@test-check_urls.R#21) 
  2. Failure: (unknown) (@test-check_urls.R#23) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In as.list(X) :
    closing unused connection 5 (https://raw.githubusercontent.com/keberwein/baseballdatabank/master/core/AllstarFull.csv)
  2: In as.list(X) :
    closing unused connection 4 (https://raw.githubusercontent.com/chadwickbureau/baseballdatabank/master/core/AllstarFull.csv)
  Execution halted
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Package suggested but not available for checking: 'doMC'
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bayes4psy)
  Loading required package: Rcpp
  > 
  > test_check("bayes4psy")
  -- 1. Error: reaction_time compare_distributions two fits  ---------------------
  result would be too long a vector
  Backtrace:
   1. bayes4psy::compare_distributions(fit1, fit2 = fit2)
   2. bayes4psy::compare_distributions(fit1, fit2 = fit2)
   3. bayes4psy:::difference(...)
   6. mcmcse::mcse(diff_smaller)
   7. base::sapply(...)
   8. base::lapply(X = X, FUN = FUN, ...)
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: reaction_time compare_distributions two fits 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/bayesCL.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
Error(s) in re-building vignettes:
--- re-building 'BayesianNetwork.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://github.com/paulgovan/BayesianNetwork/blob/master/inst/images/Dashboard.PNG?raw=true
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/paulgovan/BayesianNetwork/blob/master/inst/images/Dashboard.PNG"
  queryString          = "?raw=true"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'BayesianNetwork.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'BayesianNetwork.Rmd'

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

Error: Vignette re-building failed.
Execution halted
NeedsCompilation field should likely be 'yes'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.7Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
Running examples in 'bdDwC-Ex.R' failed
The error most likely occurred in:

> ### Name: downloadCloudData
> ### Title: Download Darwin Cloud Data
> ### Aliases: downloadCloudData
> 
> ### ** Examples
> 
> downloadCloudData()
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(file, "rt") : cannot open the connection
Calls: downloadCloudData -> read.csv -> read.table -> file
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 132.4Mb
  sub-directories of 1Mb or more:
    include  131.5Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/biganalytics.Rcheck/00install.out' for details.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.7Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigmemory.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigreadr)
  > 
  > test_check("bigreadr")
  -- 1. Error: 'fread2' can use different types of input (@test-read.R#36)  ------
  Could not resolve host: raw.githubusercontent.com
  Backtrace:
   1. testthat::expect_identical(...)
   4. bigreadr::fread2(url)
   5. data.table::fread(input, ..., data.table = data.table, nThread = nThread)
   6. curl::curl_download(input, tmpFile, mode = "wb", quiet = !showProgress)
  
  == testthat results  ===========================================================
  [ OK: 314 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'fread2' can use different types of input (@test-read.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigreadr)
  > 
  > test_check("bigreadr")
  -- 1. Error: 'fread2' can use different types of input (@test-read.R#36)  ------
  Could not resolve host: raw.githubusercontent.com
  Backtrace:
   1. testthat::expect_identical(...)
   4. bigreadr::fread2(url)
   5. data.table::fread(input, ..., data.table = data.table, nThread = nThread)
   6. curl::curl_download(input, tmpFile, mode = "wb", quiet = !showProgress)
  
  == testthat results  ===========================================================
  [ OK: 314 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'fread2' can use different types of input (@test-read.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.9Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/bigtabulate.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BinQuasi.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bioacoustics.Rcheck/00install.out' for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BioMedR.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/bitops.Rcheck/00install.out' for details.
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
--- re-building 'Employment_and_Unemployment.Rmd' using rmarkdown
--- finished re-building 'Employment_and_Unemployment.Rmd'

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

--- re-building 'Mapping_BLS_Data.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/keberwein/keberwein.github.io/master/images/bls_img/bus_fl_map.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/keberwein/keberwein.github.io/master/images/bls_img/bus_fl_map.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Mapping_BLS_Data.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Mapping_BLS_Data.Rmd'

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

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/BonEV.Rcheck/00install.out' for details.
installed size is 59.6Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      50.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error(s) in re-building vignettes:
--- re-building 'BOSSreg.Rmd' using rmarkdown
Quitting from lines 226-227 (BOSSreg.Rmd) 
Error: processing vignette 'BOSSreg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'BOSSreg.Rmd'

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

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

> ### Name: CalculateProposalLambda
> ### Title: CalculateProposalLambda
> ### Aliases: CalculateProposalLambda
> 
> ### ** Examples
> 
> sample_data = "https://raw.githubusercontent.com/lzyacht/bpgmm-examples/master/data/sampleData.csv"
> X = utils::read.table(sample_data, header = TRUE, sep = ',')
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(file, "rt") : cannot open the connection
Calls: <Anonymous> -> file
Execution halted
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.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  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    doc   2.6Mb
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Brundle.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.0Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    article   1.9Mb
    libs      1.9Mb
Running examples in 'c14bazAAR-Ex.R' failed
The error most likely occurred in:

> ### Name: classify_material
> ### Title: Apply material classification on a *c14_date_list*
> ### Aliases: classify_material classify_material.default
> ###   classify_material.c14_date_list
> 
> ### ** Examples
> 
> classify_material(
+   example_c14_date_list,
+   quiet = TRUE
+ )
Classifying material... 
Error in curl::curl_download(input, tmpFile, mode = "wb", quiet = !showProgress) : 
  Could not resolve host: raw.githubusercontent.com
Calls: classify_material ... get_thesaurus -> %>% -> eval -> eval -> <Anonymous> -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'simple_plotting.Rmd' using rmarkdown
Quitting from lines 28-29 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:


Download failed for all databases.


--- failed re-building 'simple_plotting.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'FastRWeb'
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/caTools.Rcheck/00install.out' for details.
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cattonum)
  > 
  > test_check("cattonum")
  -- 1. Failure: conditions work correctly. (@test-conditions.R#7)  --------------
  `catto_label(foo, one_of(x1, x2))` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 254 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: conditions work correctly. (@test-conditions.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [78s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cattonum)
  > 
  > test_check("cattonum")
  -- 1. Failure: conditions work correctly. (@test-conditions.R#7)  --------------
  `catto_label(foo, one_of(x1, x2))` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 254 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: conditions work correctly. (@test-conditions.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'cb2-input-handling.Rmd' using rmarkdown
Quitting from lines 53-55 (cb2-input-handling.Rmd) 
Error: processing vignette 'cb2-input-handling.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'cb2-input-handling.Rmd'

--- re-building 'cb2-tutorial.Rmd' using rmarkdown
@BASE1-1
TATTTATTTTGCTACTTAATAATTGGGACTGTGCCCAGCGCGGCGGCAAGAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@BASE1-2
TATTTATTTTGCTACTTAATAATTGGGACTCAACTATTGCTGATCATCCTAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- finished re-building 'cb2-tutorial.Rmd'

SUMMARY: processing the following file failed:
  'cb2-input-handling.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
Found the following sources/headers with CR or CRLF line endings:
  inst/include/circglmbayes.h
Some Unix compilers require LF line endings.
Error(s) in re-building vignettes:
--- re-building 'poligrams.Rmd' using rmarkdown
--- finished re-building 'poligrams.Rmd'

--- re-building 'using_clarifai.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/soodoku/clarifai/master/inst/extdata/metro-north.jpg
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/soodoku/clarifai/master/inst/extdata/metro-north.jpg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'using_clarifai.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'using_clarifai.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/cluster.Rcheck/00install.out' for details.
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/clv.Rcheck/00install.out' for details.
Running examples in 'codemetar-Ex.R' failed
The error most likely occurred in:

> ### Name: codemeta_validate
> ### Title: codemeta validate
> ### Aliases: codemeta_validate
> 
> ### ** Examples
> 
> ex <- system.file("examples/codemeta.json", package="codemetar")
> codemeta_validate(ex)
Error in store_val() : 
  jsonld.InvalidUrllist(code = "loading remote context failed", url = "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld", cause = "Evaluation error: Could not resolve host: raw.githubusercontent.com.")
Calls: codemeta_validate ... <Anonymous> -> <Anonymous> -> structure -> store_val
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/colorspace.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.0Mb
Running examples in 'commonmark-Ex.R' failed
The error most likely occurred in:

> ### Name: commonmark
> ### Title: Parse and render markdown text
> ### Aliases: commonmark markdown_html markdown markdown_xml markdown_man
> ###   markdown_commonmark markdown_text markdown_latex
> 
> ### ** Examples
> 
> md <- readLines("https://raw.githubusercontent.com/yihui/knitr/master/NEWS.md")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(con, "r") : cannot open the connection
Calls: readLines -> file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>


--- failed re-building 'commonsMath.Rmd'

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

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

> ### Name: fetch.config
> ### Title: Fetch configuration file and generate a merged list
> ### Aliases: fetch.config
> 
> ### ** Examples
> 
> links <- c(paste0('https://raw.githubusercontent.com/JhuangLab', 
+ '/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'), 
+ paste0('https://raw.githubusercontent.com/JhuangLab/BioInstaller', 
+ '/master/inst/extdata/config/db/db_main.toml'), 
+ system.file('extdata', 'config.toml', package = 'configr'))
> x <- fetch.config(links)
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Warning in download.file(link, config.download.tmp) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in download.file(link, config.download.tmp) : 
  cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Calls: fetch.config -> download.file
Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(configr)
  > library(stringr)
  > 
  > 
  > test_check("configr")
  trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
  -- 1. Error: fetch.config (@test_m_fetch.R#5)  ---------------------------------
  cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
  Backtrace:
   1. configr::fetch.config(links)
   2. utils::download.file(link, config.download.tmp)
  
  == testthat results  ===========================================================
  [ OK: 281 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: fetch.config (@test_m_fetch.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'configr.Rmd' using rmarkdown
trying URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
Quitting from lines 96-101 (configr.Rmd) 
Error: processing vignette 'configr.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/JhuangLab/BioInstaller/master/inst/extdata/config/db/db_annovar.toml'
--- failed re-building 'configr.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      1.5Mb
Package suggested but not available for checking: 'ProData'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    help   1.6Mb
Error(s) in re-building vignettes:
--- re-building 'corrgram_cov2cor.Rmd' using rmarkdown
--- finished re-building 'corrgram_cov2cor.Rmd'

--- re-building 'corrgram_examples.Rmd' using rmarkdown
Quitting from lines 231-248 (corrgram_examples.Rmd) 
Error: processing vignette 'corrgram_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'corrgram_examples.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
makeX_eset: no visible global function definition for 'model.matrix'
normFit: no visible binding for global variable 'lm'
normFit: no visible binding for global variable 'sd'
normFit: no visible global function definition for 'lm'
normPred: no visible binding for global variable 'predict'
normPred: no visible global function definition for 'predict'
normPred: no visible binding for global variable 'median'
plot.nFit: no visible global function definition for 'par'
plot.nFit: no visible global function definition for 'barplot'
plot.nFit: no visible global function definition for 'legend'
show_nfit: no visible global function definition for 'anova'
show_nfit: no visible global function definition for 'residuals'
show_nfit: no visible global function definition for 'fitted'
standardsFit: no visible binding for global variable 'lm'
standardsFit: no visible global function definition for 'resid'
standardsFit: no visible global function definition for
  'compareVersion'
standardsPred: no visible global function definition for 'predict'
makeX,ExpressionSet-character: no visible global function definition
  for 'model.matrix'
plot,nFit: no visible global function definition for 'par'
plot,nFit: no visible global function definition for 'barplot'
plot,nFit: no visible global function definition for 'legend'
show,nFit: no visible global function definition for 'anova'
show,nFit: no visible global function definition for 'residuals'
show,nFit: no visible global function definition for 'fitted'
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'detect-crop-rows.Rmd' using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    convolve, spectrum

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

    frame

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

    save.image


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: 'EBImage'

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

    channel, dilate, display, erode, resize, watershed

Warning in .loadFun(files, ...) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Quitting from lines 36-38 (detect-crop-rows.Rmd) 
Error: processing vignette 'detect-crop-rows.Rmd' failed with diagnostics:
object is NULL
--- failed re-building 'detect-crop-rows.Rmd'

SUMMARY: processing the following file failed:
  'detect-crop-rows.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'CrossScreening-vignette.Rnw' using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'read gender'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 278-280 (CrossScreening-vignette.Rnw) 
Error: processing vignette 'CrossScreening-vignette.Rnw' failed with diagnostics:
cannot open the connection
--- failed re-building 'CrossScreening-vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/curl.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'cutpointr.Rmd' using rmarkdown
Quitting from lines 181-184 (cutpointr.Rmd) 
Error: processing vignette 'cutpointr.Rmd' failed with diagnostics:
there is no package called 'registry'
--- failed re-building 'cutpointr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   1.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   1.9Mb
.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.
Error(s) in re-building vignettes:
--- re-building 'get_started.Rmd' using rmarkdown
Quitting from lines 50-72 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'get_started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'creating_data_packages_in_r.Rmd' using rmarkdown
Quitting from lines 56-59 (creating_data_packages_in_r.Rmd) 
Error: processing vignette 'creating_data_packages_in_r.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'creating_data_packages_in_r.Rmd'

--- re-building 'using_data_packages_in_r.Rmd.Rmd' using rmarkdown
Quitting from lines 74-76 (using_data_packages_in_r.Rmd.Rmd) 
Error: processing vignette 'using_data_packages_in_r.Rmd.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'using_data_packages_in_r.Rmd.Rmd'

SUMMARY: processing the following files failed:
  'creating_data_packages_in_r.Rmd' 'using_data_packages_in_r.Rmd.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
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:11027 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DealGPL570.Rcheck/00install.out' for details.
.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/4.0/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building 'custom.Rmd' using rmarkdown
Quitting from lines 77-85 (custom.Rmd) 
Error: processing vignette 'custom.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'custom.Rmd'

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

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Error(s) in re-building vignettes:
--- re-building 'graphviz-mermaid.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/rich-iannone/DiagrammeR/master/man/figures/node_attributes_2x.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/rich-iannone/DiagrammeR/master/man/figures/node_attributes_2x.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'graphviz-mermaid.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'graphviz-mermaid.Rmd'

--- re-building 'node-edge-data-frames.Rmd' using rmarkdown
--- finished re-building 'node-edge-data-frames.Rmd'

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

--- re-building 'simple-graphs-ndfs-edfs.Rmd' using rmarkdown
--- finished re-building 'simple-graphs-ndfs-edfs.Rmd'

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

SUMMARY: processing the following file failed:
  'graphviz-mermaid.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'did-basics.Rmd' using rmarkdown
Error: processing vignette 'did-basics.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 2, column 9 found unknown escape character at line 2, column 46

--- failed re-building 'did-basics.Rmd'

SUMMARY: processing the following file failed:
  'did-basics.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
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:11109 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11109 (sockconn)
Execution halted
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:11246 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11246 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/digest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/DistributionOptimization.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dmdScheme.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rPython'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'dplyrAssist.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/cardiomoon/dplyrAssist/master/man/figures/1.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/cardiomoon/dplyrAssist/master/man/figures/1.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'dplyrAssist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'dplyrAssist.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/dplyr.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
    libs   1.2Mb
Error(s) in re-building vignettes:
--- re-building 'eAnalytics.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://github.com/paulgovan/eAnalytics/blob/master/inst/images/Dashboard.png?raw=true
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/paulgovan/eAnalytics/blob/master/inst/images/Dashboard.png"
  queryString          = "?raw=true"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'eAnalytics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'eAnalytics.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running examples in 'echarts4r-Ex.R' failed
The error most likely occurred in:

> ### Name: e_geo
> ### Title: Geo
> ### Aliases: e_geo
> 
> ### ** Examples
> 
> flights <- read.csv(
+   paste0("https://raw.githubusercontent.com/plotly/datasets/",
+          "master/2011_february_aa_flight_paths.csv")
+ )
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'editData.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/cardiomoon/editData/master/man/figures/1.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/cardiomoon/editData/master/man/figures/1.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'editData.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'editData.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/EditImputeCont.Rcheck/00install.out' for details.
Running examples in 'eechidna-Ex.R' failed
The error most likely occurred in:

> ### Name: aec_add_carto_f
> ### Title: aec_add_carto_f - computes and binds the cartogram coordinates
> ###   to original data
> ### Aliases: aec_add_carto_f
> 
> ### ** Examples
> 
> library(eechidna)
> 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)
> 
> nat_map16 <- nat_map_download(2016)
trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/nat_map16.rda'
Warning in utils::download.file(url_git, tmp, ...) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in utils::download.file(url_git, tmp, ...) : 
  cannot open URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/nat_map16.rda'
Calls: nat_map_download -> <Anonymous>
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eechidna)
  > 
  > test_check("eechidna")
  trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/fp_pp.rda'
  -- 1. Error: Division names are the same across vote types - polling booth (@tes
  cannot open URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/fp_pp.rda'
  Backtrace:
   1. eechidna::firstpref_pollingbooth_download()
   2. utils::download.file(...)
  
  == testthat results  ===========================================================
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Division names are the same across vote types - polling booth (@test-election.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'eechidna-intro.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

trying URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/tpp_pp.rda'
Quitting from lines 112-123 (eechidna-intro.Rmd) 
Error: processing vignette 'eechidna-intro.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/ropenscilabs/eechidna/raw/master/extra-data/tpp_pp.rda'
--- failed re-building 'eechidna-intro.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error(s) in re-building vignettes:
--- re-building 'EHRtemporalVariability.Rmd' using rmarkdown
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

Quitting from lines 93-95 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'EHRtemporalVariability.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
Found the following significant warnings:
  emmix.cpp:351:195: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/EMMIXgene.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
Error(s) in re-building vignettes:
--- re-building 'eph.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 in readRDS(gzcon(url(link))) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Warning in get_microdata(year = 2001, wave = 2, type = "individual") :
  No se pudo descargar la base de year 2001,trimester NA, wave 2, type individual.
Mensaje: problema con la descarga. Posiblemente un error de la conexion a internet

Quitting from lines 101-103 (eph.Rmd) 
Error: processing vignette 'eph.Rmd' failed with diagnostics:
object 'Var2' not found
--- failed re-building 'eph.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [69s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eplusr)
  > eplusr_option(verbose_info = FALSE)
  $verbose_info
  [1] FALSE
  
  > 
  > test_check("eplusr")
  trying URL 'https://raw.githubusercontent.com/NREL/EnergyPlus/v9.2.0/idd/V8-9-0-Energy%2B.idd'
  -- 1. Error: Transition Helper (@test_transition.R#71)  ------------------------
  cannot open URL 'https://raw.githubusercontent.com/NREL/EnergyPlus/v9.2.0/idd/V8-9-0-Energy%2B.idd'
  Backtrace:
    1. testthat::expect_silent(...)
    9. eplusr:::trans_preprocess(idf, 8.9, "Construction")
   10. eplusr::use_idd(version, "auto")
   11. eplusr::download_idd(ver, dir = tempdir())
   12. eplusr:::download_file(url, dest)
   13. utils::download.file(url, dest, mode = "wb")
  
  == testthat results  ===========================================================
  [ OK: 1064 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Transition Helper (@test_transition.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'eplusr.Rmd' using rmarkdown
Quitting from lines 137-138 (eplusr.Rmd) 
Error: processing vignette 'eplusr.Rmd' failed with diagnostics:
Cannot find the file(s): "../man/figures/class_structure.png"
--- failed re-building 'eplusr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running examples in 'eqn2svg-Ex.R' failed
The error most likely occurred in:

> ### Name: eqn2svg
> ### Title: Convert a LaTeX math formula to an SVG object
> ### Aliases: eqn2svg
> 
> ### ** Examples
> 
> # Take LaTeX code for the Heaviside
> # Function and convert that to SVG
> heaviside <-
+   eqn2svg(
+     eqn = l_time_domain[25],
+     preview = FALSE
+   )
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: eqn2svg -> readLines -> file
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: smart_download
> ### Title: Download only those files that don't already exist
> ### Aliases: smart_download
> 
> ### ** Examples
> 
> cars <- etl("mtcars")
No database was specified so I created one for you at:
D:\temp\RtmpeIsQg3\file4f3822285f68.sqlite3
> urls <- c("https://raw.githubusercontent.com/beanumber/etl/master/etl.Rproj",
+ "https://www.reddit.com/robots.txt")
> smart_download(cars, src = urls)
Downloading 2 new files.  0 untouched.
trying URL 'https://raw.githubusercontent.com/beanumber/etl/master/etl.Rproj'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'https://raw.githubusercontent.com/beanumber/etl/master/etl.Rproj'
Calls: smart_download -> mapply -> <Anonymous>
Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  -- 1. Failure: Countrycodes use eurostat for missing (@test-all.R#105)  --------
  suppressWarnings(...) not equal to c("Finland", "Germany", "European Union - 28 countries").
  1/3 mismatches
  x[3]: "European Union - 28 countries (2013-2020)"
  y[3]: "European Union - 28 countries"
  
  trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Froad_pa_buscoa.tsv.gz'
  Content type 'application/octet-stream;charset=UTF-8' length 5176 bytes
  ==================================================
  downloaded 5176 bytes
  
  == testthat results  ===========================================================
  [ OK: 3 | SKIPPED: 20 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Countrycodes use eurostat for missing (@test-all.R#105) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(factorstochvol)
  Loading required package: stochvol
  Loading required package: coda
  > 
  > test_check("factorstochvol")
  Error in fsvsample(y, draws = draws, burnin = burnin, quiet = TRUE, factors = fs,  : 
    invalid parameters for GIG distribution: lambda=-0.9, chi=0, psi=1
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> fsvsample
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.9Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fgeo.x)
  > 
  > test_check("fgeo.x")
  trying URL 'https://github.com/forestgeo/fgeo.data/raw/master/data/unique_id.rda'
  -- 1. Error: download_data with `destfile = NULL` it reads data (@test-download_
  cannot open URL 'https://github.com/forestgeo/fgeo.data/raw/master/data/unique_id.rda'
  Backtrace:
   1. testthat::expect_is(download_data("unique_id"), "data.frame")
   4. fgeo.x::download_data("unique_id")
   6. fgeo.x:::`_f`(x = x, destfile = destfile)
   7. utils::download.file(data_url(x), tmp)
  
  trying URL 'https://github.com/forestgeo/fgeo.data/raw/master/data/unique_id.rda'
  -- 2. Error: download_data with non-NULL `destfile` downloads to `destfile` (@te
  cannot open URL 'https://github.com/forestgeo/fgeo.data/raw/master/data/unique_id.rda'
  Backtrace:
   1. fgeo.x::download_data("unique_id", destfile = tmp)
   3. fgeo.x:::`_f`(x = x, destfile = destfile)
   4. utils::download.file(data_url(x), destfile = destfile)
  
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: download_data with `destfile = NULL` it reads data (@test-download_data.R#18) 
  2. Error: download_data with non-NULL `destfile` downloads to `destfile` (@test-download_data.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'a-c.R' [25s]
  Running 'd.R' [31s]
  Running 'e.R' [106s]
  Running 'f-z.R' [57s]
Running the tests in 'tests/d.R' failed.
Complete output:
  > library(testthat)
  > library(fingertipsR)
  > 
  > test_check("fingertipsR", filter = "^[d]")
  -- 1. Failure: warnings work correctly (@test-deprivation.R#43)  ---------------
  `deprivation_decile(AreaTypeID = 120, Year = 2015)` did not produce any warnings.
  
  == testthat results  ===========================================================
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: warnings work correctly (@test-deprivation.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
Running examples in 'fivethirtyeight-Ex.R' failed
The error most likely occurred in:

> ### Name: comic_characters
> ### Title: Comic Books Are Still Made By Men, For Men And About Men
> ### Aliases: comic_characters
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To obtain the entire dataset, run the following code:
> library(readr)
> 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(tidyr)
> library(lubridate)

Attaching package: 'lubridate'

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

    date

> library(janitor)

Attaching package: 'janitor'

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

    chisq.test, fisher.test

> 
> # Get DC characters:
> comic_characters_dc <- 
+   "https://github.com/fivethirtyeight/data/raw/master/comic-characters/dc-wikia-data.csv" %>% 
+   read_csv() %>% 
+   clean_names() %>% 
+   mutate(publisher = "DC")
Error in open.connection(con, "rb") : 
  Could not resolve host: raw.githubusercontent.com
Calls: %>% ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'fivethirtyeight.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

Parsed with column specification:
cols(
  .default = col_character(),
  ARTICLE_DATE = col_date(format = ""),
  DATAFRAME_NROWS = col_number(),
  DATAFRAME_NCOLS = col_double()
)
See spec(...) for full column specifications.
--- finished re-building 'fivethirtyeight.Rmd'

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

Attaching package: 'ggplot2'

The following object is masked _by_ '.GlobalEnv':

    scale_fill_discrete


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: 'gridExtra'

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

    combine

Quitting from lines 264-267 (tame.Rmd) 
Error: processing vignette 'tame.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'tame.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Package which this enhances but not available for checking: 'doMC'
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/forestFloor.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.5Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(freetypeharfbuzz)
  > 
  > test_check("freetypeharfbuzz")
  -- 1. Failure: string metrics are computed for various edge cases (@test-string-
  `metrics` not equal to c(width = w, height = h, ascent = a, descent = d).
  2/4 mismatches (average diff: 1e-04)
  [2] 1.28 - 1.28 == 1e-04
  [3] 1.28 - 1.28 == 1e-04
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: string metrics are computed for various edge cases (@test-string-info.R#52) 
  
  Error: testthat unit tests 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  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/FunctionalNetworks.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.1Mb
    proj     5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/GeneBook.Rcheck/00install.out' for details.
Warnings in file 'R/utils.R':
  unable to translate '<U+00E9>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+2019>' to native encoding
Found the following significant warnings:
  runMCMCfunc.cpp:40:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:45: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:44: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:47: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/geoCount.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
Running examples in 'geojsonlint-Ex.R' failed
The error most likely occurred in:

> ### Name: geojson_hint
> ### Title: Validate GeoJSON using geojsonhint Javascript library
> ### Aliases: geojson_hint
> 
> ### ** Examples
> 
> geojson_hint('{"type": "FooBar"}')
[1] FALSE
> geojson_hint('{ "type": "FeatureCollection" }')
[1] FALSE
> geojson_hint(
+   '{"type":"Point","geometry":{"type":"Point","coordinates":[-80,40]},"properties":{}}'
+ )
[1] FALSE
> 
> # A file
> file <- system.file("examples", "zillow_or.geojson", package = "geojsonlint")
> geojson_hint(as.location(file))
[1] FALSE
> 
> # A URL
> url <- "https://raw.githubusercontent.com/glynnbird/usstatesgeojson/master/california.geojson"
> geojson_hint(as.location(url))
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) : 
  Could not resolve host: raw.githubusercontent.com
Calls: geojson_hint ... <Anonymous> -> <Anonymous> -> crul_fetch -> <Anonymous>
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         8.9Mb
    extdata   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Running examples in 'GetDFPData-Ex.R' failed
The error most likely occurred in:

> ### Name: gdfpd.fix.DFP.dataframes
> ### Title: Fix dataframe for version issues and inflation measures
> ###   (internal)
> ### Aliases: gdfpd.fix.DFP.dataframes
> 
> ### ** Examples
> 
> #'
> # get example data from RData file
> my.f <- system.file('extdata/Example_DFP_Report_Petrobras.RData', package = 'GetDFPData')
> load(my.f)
> 
> df.assets <- df.reports$fr.assets[[1]]
> df.inflation <- gdfpd.get.inflation.data('dollar', do.cache = FALSE)
Error in open.connection(con, "rb") : 
  Could not resolve host: raw.githubusercontent.com
Calls: gdfpd.get.inflation.data ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ggformula-blog.Rmd' using rmarkdown
--- finished re-building 'ggformula-blog.Rmd'

--- re-building 'ggformula.Rmd' using rmarkdown
Warning: Computation failed in `stat_density2d()`:
missing value where TRUE/FALSE needed
Quitting from lines 610-627 (ggformula.Rmd) 
Error: processing vignette 'ggformula.Rmd' failed with diagnostics:
'nchar()' requires a character vector
--- failed re-building 'ggformula.Rmd'

--- re-building 'learn-more.Rmd' using rmarkdown
--- finished re-building 'learn-more.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ggplotAssist.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/cardiomoon/ggplotAssistFigures/master/1.jpg
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/cardiomoon/ggplotAssistFigures/master/1.jpg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'ggplotAssist.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'ggplotAssist.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/ggrepel.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'ggseas.Rmd' using rmarkdown
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building 'ggseas.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Running examples in 'githubinstall-Ex.R' failed
The error most likely occurred in:

> ### Name: gh_suggest
> ### Title: Suggest Github Repository from a Incomplete Name
> ### Aliases: gh_suggest
> 
> ### ** Examples
> 
> gh_suggest("AnomalyDetection")
Error in curl::curl_download(input, tmpFile, mode = "wb", quiet = !showProgress) : 
  Could not resolve host: raw.githubusercontent.com
Calls: gh_suggest ... get_package_list -> gh_update_package_list -> fread -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'githubinstall.Rmd' using rmarkdown
Quitting from lines 230-231 (githubinstall.Rmd) 
Error: processing vignette 'githubinstall.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'githubinstall.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc         1.1Mb
    libs       21.2Mb
    test_data   1.2Mb
plot.glmulti: no visible global function definition for 'windows'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
Undefined global functions or variables:
  regsubsets windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
Package suggested but not available for checking: 'cplexAPI'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/glue.Rcheck/00install.out' for details.
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.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.
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/gpuR.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'dse1'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/gtools.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'gunsales.Rmd' using rmarkdown
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
Process terminated
--- failed re-building 'gunsales.Rmd'

SUMMARY: processing the following file failed:
  'gunsales.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  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc           2.7Mb
    htmlwidgets   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.5Mb
    CWrappers_1.10.3   2.4Mb
    libs               6.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.0Mb
Running 'testthat.R' [49s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hettx)
  > 
  > test_check("hettx")
  -- 1. Error: Main complier methods work (@test_estimate_systematic.R#99)  ------
  min(n11, n10, n01, n00) > 1 is not TRUE
  Backtrace:
   1. hettx::estimate_systematic(...)
   2. hettx:::est.beta.LATE(...)
   3. base::stopifnot(min(n11, n10, n01, n00) > 1)
  
  == testthat results  ===========================================================
  [ OK: 29 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Main complier methods work (@test_estimate_systematic.R#99) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   1.5Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Running examples in 'httr-Ex.R' failed
The error most likely occurred in:

> ### Name: write_stream
> ### Title: Process output in a streaming manner.
> ### Aliases: write_stream
> 
> ### ** Examples
> 
> GET(
+   "https://github.com/jeroen/data/raw/gh-pages/diamonds.json",
+   write_stream(function(x) {
+     print(length(x))
+     length(x)
+   })
+ )
Error in open.connection(con, "rbf") : 
  Could not resolve host: raw.githubusercontent.com
Calls: GET ... request_fetch.write_stream -> <Anonymous> -> open -> open.connection
Execution halted
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/igraph.Rcheck/00install.out' for details.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(imgpalr)
  > 
  > test_check("imgpalr")
  -- 1. Error: image_load loads file (@test-load.R#12)  --------------------------
  cannot open URL 'https://raw.githubusercontent.com/leonawicz/imgpalr/master/inst/blue-yellow.png'
  Backtrace:
   1. testthat::expect_is(...)
   4. imgpalr::image_load(paste0(url, basename(x[1])))
   5. downloader::download(file, destfile = tmp, quiet = TRUE, mode = "wb")
   8. utils::download.file(url, method = method, ...)
  
  == testthat results  ===========================================================
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: image_load loads file (@test-load.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IncDTW)
  
  Attaching package: 'IncDTW'
  
  The following object is masked from 'package:grDevices':
  
      cm
  
  The following objects are masked from 'package:base':
  
      norm, scale
  
  > 
  > test_check("IncDTW")
  -- 1. Failure: Double Incremental Matrix EQUAL Scratch (@test_dtw.R#308)  ------
  result0$dm not equal to result2$dm.
  1/132 mismatches
  [27] 3 - 2 == 1
  
  [1] 13265
  == testthat results  ===========================================================
  [ OK: 168 | SKIPPED: 14 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Double Incremental Matrix EQUAL Scratch (@test_dtw.R#308) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'Inflation-Ex.R' failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
The binaries provided by 'x13binary' do not work on this
machine. To get more information, run:
  x13binary::checkX13binary()

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
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
  'plot'
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 plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
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 'iotools-Ex.R' failed
The error most likely occurred in:

> ### Name: idstrsplit
> ### Title: Create an iterator for splitting binary or character input into
> ###   a dataframe
> ### Aliases: idstrsplit
> ### Keywords: iterator
> 
> ### ** Examples
> 
> col_names <- names(iris)
> write.csv(iris, file="iris.csv", row.names=FALSE)
> it <- idstrsplit("iris.csv", col_types=c(rep("numeric", 4), "character"), 
+                  sep=",")
> # Get the elements
> iris_read <- it$nextElem()[-1,]
> # or with the iterators package
> # nextElem(it)
> names(iris_read) <- col_names
> print(head(iris_read))
  Sepal.Length Sepal.Width Petal.Length Petal.Width  Species
2          5.1         3.5          1.4         0.2 "setosa"
3          4.9         3.0          1.4         0.2 "setosa"
4          4.7         3.2          1.3         0.2 "setosa"
5          4.6         3.1          1.5         0.2 "setosa"
6          5.0         3.6          1.4         0.2 "setosa"
7          5.4         3.9          1.7         0.4 "setosa"
> unlink("iris.csv")
> 
> 
> 
> cleanEx()
Error: connections left open:
	iris.csv (file)
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
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] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11389 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11389 (sockconn)
Execution halted
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:11347 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11347 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/irlba.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(itunesr)
  > 
  > test_check("itunesr")
  -- 1. Error: The output dataframe Type is  (@test-fun.R#7)  --------------------
  attempt to set an attribute on NULL
  Backtrace:
   1. testthat::expect_equal(...)
   4. itunesr::getReviews("297606951", "in", 2)
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: The output dataframe Type is  (@test-fun.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jackalope.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/jsonlite.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/KernSmooth.Rcheck/00install.out' for details.
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  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.4Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.9Mb
    proj   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lattice.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lazyeval.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'lbfgsb3c.Rmd' using rmarkdown
Quitting from lines 139-237 (lbfgsb3c.Rmd) 
Error: processing vignette 'lbfgsb3c.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'lbfgsb3c.Rmd'

SUMMARY: processing the following file failed:
  'lbfgsb3c.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
Error(s) in re-building vignettes:
--- re-building 'LDATS_codebase.Rmd' using rmarkdown
--- finished re-building 'LDATS_codebase.Rmd'

--- re-building 'paper-comparison.Rmd' using rmarkdown
trying URL 'https://raw.githubusercontent.com/emchristensen/Extreme-events-LDA/master/rodent_LDA_analysis.r'
Quitting from lines 108-135 (paper-comparison.Rmd) 
Error: processing vignette 'paper-comparison.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/emchristensen/Extreme-events-LDA/master/rodent_LDA_analysis.r'
--- failed re-building 'paper-comparison.Rmd'

--- re-building 'rodents-example.Rmd' using rmarkdown
--- finished re-building 'rodents-example.Rmd'

SUMMARY: processing the following file failed:
  'paper-comparison.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Error(s) in re-building vignettes:
--- re-building 'ElasticNet.Rmd' using rmarkdown
--- finished re-building 'ElasticNet.Rmd'

--- re-building 'GxE_testing.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/AlexiaJM/LEGIT/master/images/GxE_testing_strong.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/AlexiaJM/LEGIT/master/images/GxE_testing_strong.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'GxE_testing.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'GxE_testing.Rmd'

--- re-building 'LEGIT.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/AlexiaJM/LEGIT/master/images/LEGIT.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/AlexiaJM/LEGIT/master/images/LEGIT.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'LEGIT.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'LEGIT.Rmd'

SUMMARY: processing the following files failed:
  'GxE_testing.Rmd' 'LEGIT.Rmd'

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'rsyslog'
Package unavailable to check Rd xrefs: 'rsyslog'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      2.4Mb
Error(s) in re-building vignettes:
--- re-building 'lidR-LAS-class.Rmd' using rmarkdown
--- finished re-building 'lidR-LAS-class.Rmd'

--- re-building 'lidR-LAScatalog-class.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/Jean-Romain/storage/master/CATALOG/mapview-vignette.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/Jean-Romain/storage/master/CATALOG/mapview-vignette.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'lidR-LAScatalog-class.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'lidR-LAScatalog-class.Rmd'

--- re-building 'lidR-catalog-apply-examples.Rmd' using rmarkdown
--- finished re-building 'lidR-catalog-apply-examples.Rmd'

--- re-building 'lidR-computation-speed-LAScatalog.Rmd' using rmarkdown
--- finished re-building 'lidR-computation-speed-LAScatalog.Rmd'

SUMMARY: processing the following file failed:
  'lidR-LAScatalog-class.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/lsei.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   1.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
    proj   5.0Mb
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> cleanEx()
> nameEx("interactive_threshold")
> ### * interactive_threshold
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: interactive_threshold
> ### Title: interactive thresholding
> ### Aliases: interactive_threshold
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.1 0.09 1.21 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 41.2Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.7Mb
Running examples in 'markmyassignment-Ex.R' failed
The error most likely occurred in:

> ### Name: mark_my_assignment
> ### Title: Mark assignment in global environment
> ### Aliases: mark_my_assignment
> 
> ### ** Examples
> 
> assignment_path <- 
+   file.path(system.file(package = "markmyassignment"), "extdata", "example_assignment01.yml")
> set_assignment(assignment_path)
Error in path_type(file.path(base_path, sub_path)) : 
  'D:/RCompile/CRANpkg/lib/4.0/markmyassignment/extdata/https://raw.githubusercontent.com/MansMeg/markmyassignment/master/inst/extdata/example_task1.R' is an incorrect path.
Calls: set_assignment ... download_assignment -> get_assignment_full_subpath -> path_type
Execution halted
Error(s) in re-building vignettes:
--- re-building 'markmyassignment-teacher.Rmd' using rmarkdown
--- finished re-building 'markmyassignment-teacher.Rmd'

--- re-building 'markmyassignment.Rmd' using rmarkdown
Quitting from lines 43-46 (markmyassignment.Rmd) 
Error: processing vignette 'markmyassignment.Rmd' failed with diagnostics:
'D:/RCompile/CRANpkg/lib/4.0/markmyassignment/extdata/https://raw.githubusercontent.com/MansMeg/markmyassignment/master/inst/extdata/example_task1.R' is an incorrect path.
--- failed re-building 'markmyassignment.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/MASS.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0/MatrixModels.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Matrix.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Package suggested but not available for checking: 'unix'
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs   4.1Mb
    misc   1.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.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.
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.
Found the following significant warnings:
  GLMM_Deviance.cpp:153:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance.cpp:708:11: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:173:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:780:11: warning: statement has no effect [-Wunused-value]
  GLMM_newData.cpp:183:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:161:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:626:11: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:11: warning: statement has no effect [-Wunused-value]
  NMix_updateMeansVars.cpp:516:16: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/mixAK.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.4Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   1.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.4Mb
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.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 23.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  20.9Mb
Error(s) in re-building vignettes:
--- re-building 'README.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.github.com/nielsrhansen/msgl/master/fig1.png
HttpExceptionRequest Request {
  host                 = "raw.github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/nielsrhansen/msgl/master/fig1.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'README.Rmd'

--- re-building 'msgl-getting-started.Rmd' using rmarkdown
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building 'msgl-getting-started.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error(s) in re-building vignettes:
--- re-building 'muHVT.Rmd' using rmarkdown
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.0/R.oo_1.23.0.zip'
Content type 'application/zip' length 959119 bytes (936 KB)
==================================================
downloaded 936 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.0/R.methodsS3_1.7.1.zip'
Content type 'application/zip' length 77177 bytes (75 KB)
==================================================
downloaded 75 KB

trying URL 'http://cran.us.r-project.org/bin/windows/contrib/4.0/R.utils_2.9.2.zip'
Content type 'application/zip' length 1383861 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Quitting from lines 248-251 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'muHVT.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   1.5Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [123s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(nandb)
  > 
  > test_check("nandb")
  -- 1. Failure: median and smooth filters work (@test-filters.R#7)  -------------
  round(mean(median_filter(m, na_rm = TRUE), na.rm = TRUE), 3) not equal to 3.812.
  1/1 mismatches
  [1] 3.81 - 3.81 == 0.001
  
  == testthat results  ===========================================================
  [ OK: 153 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: median and smooth filters work (@test-filters.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    1.9Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("nat.utils")
  Loading required package: nat.utils
  -- 1. Failure: common_path works (@test-fsutils.r#79)  -------------------------
  common_path(c("/a", "/b"), normalise = T) not equal to np("/").
  1/1 mismatches
  x[1]: "d:/"
  y[1]: "D:/"
  
  == testthat results  ===========================================================
  [ OK: 73 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: common_path works (@test-fsutils.r#79) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nearfar.Rcheck/00install.out' for details.
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.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.
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 'd:/Rcompile/CRANpkg/local/4.0/NestedCategBayesImpute.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'neurobase.Rmd' using rmarkdown
--- finished re-building 'neurobase.Rmd'

--- re-building 'nifti_basics.Rmd' using rmarkdown
Quitting from lines 189-219 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'nifti_basics.Rmd'

--- re-building 'simple_io.Rmd' using rmarkdown
trying URL 'https://johnmuschelli.com/open_ms_data/cross_sectional/raw/patient01/T1W.nii.gz'
Content type 'application/gzip' length 21807043 bytes (20.8 MB)
==================================================
downloaded 20.8 MB

--- finished re-building 'simple_io.Rmd'

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

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

> ### Name: eigenComputes
> ### Title: Computes Eigenvalues According to the Data Type
> ### Aliases: eigenComputes
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> # .......................................................
> # Different data types
> # Vector of eigenvalues
>   data(dFactors)
>   x1 <- dFactors$Cliff1$eigenvalues
>   eigenComputes(x1)
 [1]  2.842  1.080  0.640  0.171  0.015 -0.008 -0.008 -0.126 -0.040 -0.066
[11] -0.111 -0.116
>   
> # Data from a data.frame
>   x2 <- data.frame(matrix(20*rnorm(100), ncol=5))
>   eigenComputes(x2, cor=TRUE,  use="everything")
[1] 1.5562290 1.3713228 1.1323986 0.6806224 0.2594272
>   eigenComputes(x2, cor=FALSE, use="everything")
[1] 527.95290 485.38169 365.44540 209.02148  84.80241
>   eigenComputes(x2, cor=TRUE,  use="everything", method="spearman")
[1] 1.486597 1.448541 1.249002 0.625795 0.190065
>   eigenComputes(x2, cor=TRUE,  use="everything", method="kendall")
[1] 1.3682956 1.3334477 1.2159607 0.7120364 0.3702597
> 
> # From a covariance matrix
>   x3 <- cov(x2)
>   eigenComputes(x3, cor=TRUE,  use="everything")
Error in switch(classType, data.frame = "data", matrix = "correlation",  : 
  EXPR must be a length 1 vector
Calls: eigenComputes -> eigenFrom
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.2Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/nlme.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Running examples in 'nlrx-Ex.R' failed
The error most likely occurred in:

> ### Name: nldoc
> ### Title: Create NetLogo documentation
> ### Aliases: nldoc
> 
> ### ** Examples
> 
> 
> # List model files (.nls subfiles are also supported)
> modelfiles <- c("https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo",
+                 "https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nls")
> 
> # Define output directory:
> outdir <- tempdir()  # adjust path to your needs
> 
> # Create documentation:
> nldoc(modelfiles = modelfiles,
+       infotab=TRUE,
+       gui=TRUE,
+       bs=TRUE,
+       outpath = outdir,
+       output_format = "html",
+       number_sections = TRUE,
+       theme = "cosmo",
+       date = date(),
+       toc = TRUE)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(con, "r") : cannot open the connection
Calls: nldoc -> nldoc_read_nlogo -> readLines -> file
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Running examples in 'nsrr-Ex.R' failed
The error most likely occurred in:

> ### Name: nsrr_version
> ### Title: NSRR Gem version online
> ### Aliases: nsrr_version nsrr_gem_version nsrr_api_version
> 
> ### ** Examples
> 
> nsrr_version()
[1] "0.1.3"
> nsrr_gem_version()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: raw.githubusercontent.com
Calls: nsrr_gem_version ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   2.7Mb
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for 'flush.console'
nwsPkgInfo: no visible global function definition for
  'packageDescription'
initialize,nwsServer: no visible global function definition for
  'make.socket'
initialize,nwsServer: no visible global function definition for
  'close.socket'
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.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 10.9Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.5Mb
    libs   2.0Mb
mapvar: no visible global function definition for 'data'
mapvar: no visible binding for global variable 'state.fips'
mapvar: no visible global function definition for 'rgb'
mapvar: no visible global function definition for 'rect'
mapvar: no visible global function definition for 'text'
rowScrape: no visible global function definition for 'tail'
rowScrape: no visible global function definition for 'head'
scrapeTable: no visible binding for global variable 'tail'
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.
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'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/OpenCL.Rcheck/00install.out' for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs   20.0Mb
    share   9.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.5Mb
    models   4.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Running 'testthat.R' [44s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(openxlsx)
  > 
  > test_check("openxlsx")
  -- 1. Error: read.xlsx from different sources (@test-read_sources.R#14)  -------
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::read.xlsx(xlsxFile)
   2. openxlsx:::read.xlsx.default(xlsxFile)
   3. openxlsx:::getFile(xlsxFile)
   4. utils::download.file(...)
  
  -- 2. Error: loadWorkbook from different sources (@test-read_sources.R#42)  ----
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::loadWorkbook(xlsxFile)
   2. openxlsx:::getFile(file)
   3. utils::download.file(...)
  
  -- 3. Error: getDateOrigin from different sources (@test-read_sources.R#62)  ---
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::getDateOrigin(xlsxFile)
   2. openxlsx:::getFile(xlsxFile)
   3. utils::download.file(...)
  
  == testthat results  ===========================================================
  [ OK: 984 | SKIPPED: 3 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: read.xlsx from different sources (@test-read_sources.R#14) 
  2. Error: loadWorkbook from different sources (@test-read_sources.R#42) 
  3. Error: getDateOrigin from different sources (@test-read_sources.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(openxlsx)
  > 
  > test_check("openxlsx")
  -- 1. Error: read.xlsx from different sources (@test-read_sources.R#14)  -------
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::read.xlsx(xlsxFile)
   2. openxlsx:::read.xlsx.default(xlsxFile)
   3. openxlsx:::getFile(xlsxFile)
   4. utils::download.file(...)
  
  -- 2. Error: loadWorkbook from different sources (@test-read_sources.R#42)  ----
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::loadWorkbook(xlsxFile)
   2. openxlsx:::getFile(file)
   3. utils::download.file(...)
  
  -- 3. Error: getDateOrigin from different sources (@test-read_sources.R#62)  ---
  cannot open URL 'https://github.com/awalker89/openxlsx/raw/master/inst/readTest.xlsx'
  Backtrace:
   1. openxlsx::getDateOrigin(xlsxFile)
   2. openxlsx:::getFile(xlsxFile)
   3. utils::download.file(...)
  
  == testthat results  ===========================================================
  [ OK: 984 | SKIPPED: 3 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: read.xlsx from different sources (@test-read_sources.R#14) 
  2. Error: loadWorkbook from different sources (@test-read_sources.R#42) 
  3. Error: getDateOrigin from different sources (@test-read_sources.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.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  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Error(s) in re-building vignettes:
--- re-building 'Over_Sampling_for_Time_Series_Classification.Rmd' using rmarkdown
Loading required package: knitcitations
Loading required package: OSTSC
Loading required package: keras
Loading required package: dummies
dummies-1.5.6 provided by Decision Patterns

Loading required package: pROC
Type 'citation("pROC")' for a citation.

Attaching package: 'pROC'

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

    cov, smooth, var

Quitting from lines 93-101 (Over_Sampling_for_Time_Series_Classification.Rmd) 
Error: processing vignette 'Over_Sampling_for_Time_Series_Classification.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'Over_Sampling_for_Time_Series_Classification.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: 'Rcplex'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Error(s) in re-building vignettes:
--- re-building 'passport.Rmd' using rmarkdown
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.2.1     v purrr   0.3.3
v tibble  2.1.3     v dplyr   0.8.4
v tidyr   1.0.2     v stringr 1.4.0
v readr   1.3.1     v forcats 0.4.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Quitting from lines 79-83 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'passport.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   1.2Mb
    doc    2.1Mb
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  13.2Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
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:11495 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11495 (sockconn)
Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(performance)
  > 
  > if (length(strsplit(packageDescription("performance")$Version, "\\.")[[1]]) > 3) {
  +   Sys.setenv("RunAllinsightTests" = "yes")
  + } else {
  +   Sys.setenv("RunAllinsightTests" = "no")
  + }
  > 
  > 
  > test_check("performance")
  -- 1. Error: (unknown) (@test-model_performance-various.R#4)  ------------------
  Could not resolve host: raw.githubusercontent.com
  Backtrace:
   1. insight::download_model("betareg_1")
   2. insight:::.download_data_github(name, url)
   3. httr::GET(url)
   4. httr:::request_perform(req, hu$handle$handle)
   6. httr:::request_fetch.write_memory(req$output, req$url, handle)
   7. curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  [ OK: 44 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-model_performance-various.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/permDep.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/phateR.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
--- re-building 'piecewiseSEM.Rmd' using rmarkdown
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Loading required package: Matrix

Attaching package: 'lme4'

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

    lmList

pandoc.exe: Could not fetch https://github.com/jslefche/jslefche.github.io/blob/master/img/example_sem.jpg?raw=true
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/jslefche/jslefche.github.io/blob/master/img/example_sem.jpg"
  queryString          = "?raw=true"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'piecewiseSEM.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'piecewiseSEM.Rmd'

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

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

--- re-building 'intro.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://github.com/ropensci/piggyback/raw/83776863b34bb1c9962154608a5af41867a0622f/man/figures/github-policy.png
HttpExceptionRequest Request {
  host                 = "github.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/ropensci/piggyback/raw/83776863b34bb1c9962154608a5af41867a0622f/man/figures/github-policy.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'intro.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'intro.Rmd'

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

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

> ### Name: pin
> ### Title: Pin Resource
> ### Aliases: pin
> 
> ### ** Examples
> 
> library(pins)
> 
> # define local board
> board_register_local(cache = tempfile())
> 
> # cache the mtcars dataset
> pin(mtcars)
> 
> # cache computation over mtcars
> mtcars[mtcars$mpg > 30,] %>%
+   pin(name = "mtefficient")
> 
> # retrieve cached pin
> pin_get("mtefficient")
                mpg cyl disp  hp drat    wt  qsec vs am gear carb
Fiat 128       32.4   4 78.7  66 4.08 2.200 19.47  1  1    4    1
Honda Civic    30.4   4 75.7  52 4.93 1.615 18.52  1  1    4    2
Toyota Corolla 33.9   4 71.1  65 4.22 1.835 19.90  1  1    4    1
Lotus Europa   30.4   4 95.1 113 3.77 1.513 16.90  1  1    5    2
> 
> # url to remote resource
> resource <- file.path("https://raw.githubusercontent.com/facebook/prophet",
+                       "master/examples/example_retail_sales.csv")
> 
> # cache remote resource
> pin(resource, name = "example_retail_sales")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: raw.githubusercontent.com
Calls: pin ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/pkgload.Rcheck/00install.out' for details.
Warnings in file 'R/HT_IVIVE_InputModule.R':
  unable to translate '	<U+03BC>m' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/IVIVEGadget.R':
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding

Warnings in file 'R/performIVIVEModule.R':
  unable to translate '<U+03BC>mol/min/10^6 hepatocytes' to native encoding
  unable to translate '<U+03BC>mol/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
  unable to translate '<U+03BC>L/min/mg Protein' to native encoding
  unable to translate '<U+03BC>L/h/mg Protein' to native encoding
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.4Mb
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  -- 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ---------
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  == testthat results  ===========================================================
  [ OK: 1370 | SKIPPED: 45 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/plyr.Rcheck/00install.out' for details.
Running examples in 'pollimetry-Ex.R' failed
The error most likely occurred in:

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

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Could not resolve host: raw.githubusercontent.com
Calls: bodysize ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0/PPRL.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'introduction_to_prcr.Rmd' using rmarkdown
################################
Clustering data for iteration 2
Clustering data for iteration 3
Clustering data for iteration 4
################################
################################
################################
Clustering data for iteration 1
Quitting from lines 62-70 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
x The columns `2`, `2`, `1`, `2`, `2`, etc. don't exist.
--- failed re-building 'introduction_to_prcr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'preputils.Rmd' using rmarkdown
Error: processing vignette 'preputils.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 3, column 7 found unknown escape character at line 10, column 4

--- failed re-building 'preputils.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
    proj   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Error(s) in re-building vignettes:
--- re-building 'overview.Rmd' using rmarkdown
pandoc-citeproc.exe: Error parsing XML file https://raw.githubusercontent.com/bwiernik/zotero-tools/master/apa-short-authors.csl: HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/bwiernik/zotero-tools/master/apa-short-authors.csl"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
pandoc.exe: Error running filter D:/compiler/pandoc/pandoc-citeproc.exe
Filter returned error status 1
Error: processing vignette 'overview.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
--- failed re-building 'overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc        4.7Mb
    examples   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'PTXQC-Basic_Guide_for_R_users.Rmd' using rmarkdown
--- finished re-building 'PTXQC-Basic_Guide_for_R_users.Rmd'

--- re-building 'PTXQC-CustomizeReport.Rmd' using rmarkdown
--- finished re-building 'PTXQC-CustomizeReport.Rmd'

--- re-building 'PTXQC-DragNDrop.Rmd' using rmarkdown
--- finished re-building 'PTXQC-DragNDrop.Rmd'

--- re-building 'PTXQC-FAQ.Rmd' using rmarkdown
--- finished re-building 'PTXQC-FAQ.Rmd'

--- re-building 'PTXQC-Input_And_Output_Data.Rmd' using rmarkdown
--- finished re-building 'PTXQC-Input_And_Output_Data.Rmd'

--- re-building 'PTXQC-ListOfMetrics.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/cbielow/PTXQC/mzTab_support/inst/reportTemplate/modes_UpSet.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/cbielow/PTXQC/mzTab_support/inst/reportTemplate/modes_UpSet.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'PTXQC-ListOfMetrics.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'PTXQC-ListOfMetrics.Rmd'

SUMMARY: processing the following file failed:
  'PTXQC-ListOfMetrics.Rmd'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/purrr.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > print(Sys.getenv("NOT_CRAN"))
  [1] ""
  > testthat::test_check("pxweb")
  Loading required package: pxweb
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014-2018 Mans Magnusson, Leo Lahti et al.
  https://github.com/ropengov/pxweb
  
  -- 1. Error: pxweb_api_catalogue (@test-pxweb_api_catalogue.R#10)  -------------
  Could not resolve host: raw.githubusercontent.com
  Backtrace:
    1. testthat::expect_silent(pxacgh <- pxweb:::pxweb_api_catalogue_from_github("test"))
    9. pxweb:::pxweb_api_catalogue_from_github("test")
   10. httr::GET(url_raw)
   11. httr:::request_perform(req, hu$handle$handle)
   13. httr:::request_fetch.write_memory(req$output, req$url, handle)
   14. curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 50 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: pxweb_api_catalogue (@test-pxweb_api_catalogue.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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
Error(s) in re-building vignettes:
--- re-building 'bootstrap-cluster.Rmd' using rmarkdown
Quitting from lines 42-47 (bootstrap-cluster.Rmd) 
Error: processing vignette 'bootstrap-cluster.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'bootstrap-cluster.Rmd'

--- re-building 'd-variate-analysis.Rmd' using rmarkdown
--- finished re-building 'd-variate-analysis.Rmd'

--- re-building 'recla-analysis.Rmd' using rmarkdown
pandoc-citeproc: reference broman2019rqlt2 not found
--- finished re-building 'recla-analysis.Rmd'

SUMMARY: processing the following file failed:
  'bootstrap-cluster.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.3Mb
    libs   3.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.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.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.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 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
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.
Error(s) in re-building vignettes:
--- re-building 'Vignette.Rmd' using rmarkdown
Warning in roc.default(response, predictors[, 1], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Warning in coords.roc(rocobj, "all", ret = c("tp")) :
  The 'transpose' argument to FALSE by default since pROC 1.16. Set transpose = TRUE explicitly to revert to the previous behavior, or transpose = TRUE to silence this warning. Type help(coords_transpose) for additional information.
Warning in coords.roc(rocobj, "all", ret = "fp") :
  The 'transpose' argument to FALSE by default since pROC 1.16. Set transpose = TRUE explicitly to revert to the previous behavior, or transpose = TRUE to silence this warning. Type help(coords_transpose) for additional information.
Quitting from lines 411-412 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'Vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   6.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.0Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/randstr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RANN.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rappdirs.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
Loading required package: Rcpp

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 object is masked from 'package:base':

    date

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 33-51 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    etc    1.9Mb
    po     1.2Mb
Error(s) in re-building vignettes:
--- re-building 'raustats_introduction.Rmd' using rmarkdown
Loading required package: readxl
Attaching package: 'raustats'
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Sep%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Sep%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/6401.0Dec%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Dec%202017?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Sep%202017?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/1270.0.55.001July%202016?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Sep%202019?OpenDocument
Quitting from lines 734-736 (raustats_introduction.Rmd) 
Error: processing vignette 'raustats_introduction.Rmd' failed with diagnostics:
Entity 'nbsp' not defined [26]
--- failed re-building 'raustats_introduction.Rmd'

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

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

> ### Name: github
> ### Title: Retrieve raw R code from an .R file hosted on github website
> ### Aliases: github
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> github("https://github.com/hadley/vis-eda/blob/master/travel.R")
Error in open.connection(x, "rb") : 
  Could not resolve host: raw.githubusercontent.com
Calls: github ... freduce -> <Anonymous> -> read_html -> read_html.default
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rblpapi.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/Rcplex.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RcppAnnoy.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   6.2Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rcpp.Rcheck/00install.out' for details.
Warnings in file 'R/crAddins.R':
  unable to translate '<U+25B2>' to native encoding
  unable to translate '<U+25BC>' to native encoding
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RCurl.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Loading required package: sf
Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3

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 28-65 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'spelling.R' [0s]
  Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdflib)
  > 
  > test_check("rdflib")
  -- 1. Error: we can parse from a url (@test-parse-serialize.R#198)  ------------
  cannot open URL 'https://tinyurl.com/ycf95c9h'
  Backtrace:
   1. rdflib::rdf_parse("https://tinyurl.com/ycf95c9h")
   2. rdflib:::text_or_url_to_doc(doc, tmp_string)
   3. utils::download.file(x, tmp, quiet = TRUE)
  
  == testthat results  ===========================================================
  [ OK: 54 | SKIPPED: 6 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: we can parse from a url (@test-parse-serialize.R#198) 
  
  librdf error - XML parser error: Extra content at the end of the document
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for 'abline'
bestmods: no visible global function definition for 'axis'
bestmods: no visible global function definition for 'lines'
cic: no visible global function definition for 'lsfit'
cic: no visible global function definition for 'var'
cvic: no visible global function definition for 'lsfit'
cvic: no visible global function definition for 'lm'
eic: no visible global function definition for 'lsfit'
eic: no visible global function definition for 'lm'
ic.min: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'lsfit'
scoremods: no visible global function definition for 'var'
xy: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error(s) in re-building vignettes:
--- re-building 'restrictions.Rmd' using rmarkdown
Quitting from lines 129-197 (restrictions.Rmd) 
Error: processing vignette 'restrictions.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'restrictions.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: 'Rcplex'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.7Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
delete: no visible global function definition for 'menu'
doc_temp: no visible global function definition for 'menu'
html5: no visible global function definition for 'na.omit'
install_pandoc: no visible global function definition for
  'download.file'
latexlist: no visible global function definition for 'readClipboard'
new_report: no visible global function definition for 'tail'
new_report: no visible global function definition for 'head'
new_report: no visible global function definition for 'menu'
presentation: no visible global function definition for 'head'
presentation: no visible global function definition for 'tail'
presentation: no visible global function definition for 'menu'
repo2github: no visible global function definition for 'download.file'
repo2github: no visible global function definition for 'unzip'
reveal.js: no visible global function definition for 'na.omit'
strWrap: no visible global function definition for 'readClipboard'
update_bib: no visible global function definition for 'tail'
update_bib: no visible global function definition for 'menu'
Undefined global functions or variables:
  download.file head menu na.omit readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
Running 'test-all.R' [27s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > library("rerddap")
  > 
  > #Sys.setenv(RERDDAP_CACHE_PATH_SUFFIX = "rerddap")
  > cache_setup(temp_dir = TRUE)
  [1] "D:\\temp\\Rtmp8SpUrk/R/rerddap"
  > 
  > test_check("rerddap")
  -- 1. Error: convert_units works (@test-convert_units.R#15)  -------------------
  Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10015 milliseconds with 0 out of 0 bytes received
  Backtrace:
   1. testthat::expect_equal(convert_units(udunits = "degC"), "Cel")
   4. rerddap::convert_units(udunits = "degC")
   5. cli$get(query = args)
   6. private$make_request(rr)
   7. crul:::crul_fetch(opts)
   8. curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
  
  == testthat results  ===========================================================
  [ OK: 36 | SKIPPED: 19 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: convert_units works (@test-convert_units.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'rerddapXtracto-Ex.R' failed
The error most likely occurred in:

> ### Name: rxtractogon
> ### Title: Extract environmental data in a polygon using 'ERDDAP' and
> ###   'rerddap'.
> ### Aliases: rxtractogon
> 
> ### ** Examples
> 
> # toy example to show use
> # and keep execution time low
> parameter <- 'sst'
> tcoord <- c("2016-06-15")
> xcoord <- mbnms$Longitude[1:3]
> ycoord <- mbnms$Latitude[1:3]
> sanctSST <- rxtractogon (dataInfo, parameter=parameter, xcoord = xcoord,
+                          ycoord = ycoord,  tcoord= tcoord)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10013 milliseconds with 0 out of 0 bytes received
Calls: rxtractogon ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building 'UsingrerddapXtracto.Rmd' using rmarkdown
Quitting from lines 273-284 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10007 milliseconds with 0 out of 0 bytes received
--- failed re-building 'UsingrerddapXtracto.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Warning in value[[3L]](cond) :
  The configuration file could not be downloaded from GitHub, the preinstalled file in the package is used.

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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/reticulate.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   5.0Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
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  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.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/i386/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/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/i386/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'
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 i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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 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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/RKEELjars.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rlang.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rmagic.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Running 'spelling.R' [0s]
  Running 'test-all.R' [68s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > 
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  -- 1. Error: we can read nexml from a url (@test_nexml_read.R#14)  -------------
  Could not resolve host: raw.githubusercontent.com
  Backtrace:
   1. RNeXML::read.nexml(url)
   2. RNeXML:::nexml_read.character(url)
   3. httr::GET(x)
   4. httr:::request_perform(req, hu$handle$handle)
   6. httr:::request_fetch.write_memory(req$output, req$url, handle)
   7. curl::curl_fetch_memory(url, handle = handle)
  
  Done simulation(s).
  == testthat results  ===========================================================
  [ OK: 303 | SKIPPED: 42 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: we can read nexml from a url (@test_nexml_read.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0/RobExtremes.Rcheck/00install.out' for details.
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.7/ROracle.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       2.1Mb
    libs    1.7Mb
    tests   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'rpredictit-vignette.Rmd' using rmarkdown
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building 'rpredictit-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'install_guide.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/jannes-m/RQGIS/master/figures/00_express.PNG
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/jannes-m/RQGIS/master/figures/00_express.PNG"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'install_guide.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'install_guide.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Error(s) in re-building vignettes:
--- re-building 'Rraven.Rmd' using rmarkdown
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Loading required package: knitr

NOTE: functions are being 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
pandoc.exe: Could not fetch https://raw.githubusercontent.com/maRce10/Rraven/master/gifs/opt2_short_raven_correlator.gif
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/maRce10/Rraven/master/gifs/opt2_short_raven_correlator.gif"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Rraven.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Rraven.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
   #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/4.0/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 i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0/Rserve/libs/i386/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 'd:/Rcompile/CRANpkg/lib/4.0/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/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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:  3.82 0.21 4.02 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.2Mb
    libs  17.8Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/rstap.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
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) (2019-07-05 r76784)
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_3.7.0
> 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()
Running examples in 'RSwissMaps-Ex.R' failed
The error most likely occurred in:

> ### Name: map.load
> ### Title: Download additional geodata of Swiss municipalities, districts,
> ###   cantons and lakes
> ### Aliases: map.load
> 
> ### ** Examples
> 
> ## Not run:
> #Download Swiss geodata for 2017
> map.load(2017)
trying URL 'https://github.com/zumbov2/RSwissMaps/raw/master/data/mapCH2017.rda'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'https://github.com/zumbov2/RSwissMaps/raw/master/data/mapCH2017.rda'
Calls: map.load -> <Anonymous>
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/Rtsne.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    libs   1.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
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'.
Package suggested but not available for checking: 'SnakeCharmR'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error(s) in re-building vignettes:
--- re-building 'R-versus-CPP.Rmd' using rmarkdown
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'R-versus-CPP.Rmd'

SUMMARY: processing the following file failed:
  'R-versus-CPP.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
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.
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
> 
> # execute script text
> output <- scriptexec::execute('echo command1\necho command2')
> expect_equal(output$status, 0)
> expect_equal(grepl('command1', output$output), TRUE)
Error: grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
--- failed re-building 'scriptexec.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/sctransform.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/SDMTools.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
Running 'cran-tests.R' [0s]
  Running 'test-all.R' [0s]
Running the tests in 'tests/cran-tests.R' failed.
Complete output:
  > # --- Startup tests ------------------------------------------------------------
  > 
  > x13binary::checkX13binary()
  Error in x13binary::checkX13binary() : X-13 binary file not found
  Execution halted
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # for CRAN SUBMISSION:
  > # - is NEWS and DESCRIPTION up to date?
  > 
  > # - knit vignette
  > # - rhub test
  > 
  > # travisdir <- "~/git/seasonal/travis"
  > # These tests are more extensive and only need to run on travis, not on CRAN.
  > 
  > seasonal::checkX13()
  The binaries provided by 'x13binary' do not work on this
  machine. To get more information, run:
    x13binary::checkX13binary()
  
  You can set 'X13_PATH' manually if you intend to use your own
  binaries. See ?seasonal for details.
  
  No path to the binary executable of X-13 specified.
  
  You can set 'X13_PATH' manually if you intend to use your own
  binaries. See ?seasonal for details.
  
  > x13binary::checkX13binary()
  Error in x13binary::checkX13binary() : X-13 binary file not found
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
Running examples in 'seeclickfixr-Ex.R' failed
The error most likely occurred in:

> ### Name: list_places
> ### Title: Query sub-city neighborhoods in which issues can be reported.
> ### Aliases: list_places
> 
> ### ** Examples
> 
> list_places("Boston, MA",limit = 5)
Error in function (type, msg, asError = TRUE)  : 
  Unknown SSL protocol error in connection to seeclickfix.com:443 
Calls: list_places -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Running examples in 'sen2r-Ex.R' failed
The error most likely occurred in:

> ### Name: s2_tiles
> ### Title: Load Sentinel-2 tiles
> ### Aliases: s2_tiles
> 
> ### ** Examples
> 
> # Retrieve all the tiles
> s2tiles <- s2_tiles()
[2020-02-10 14:36:05] Downloading and creating the vector of Sentinel-2
       tiles (this happens once)...
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Could not resolve host: raw.githubusercontent.com
Calls: s2_tiles ... request_fetch -> request_fetch.write_disk -> <Anonymous>
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   1.5Mb
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.
installed size is 95.1Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.1Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.1Mb
Running examples in 'sim1000G-Ex.R' failed
The error most likely occurred in:

> ### Name: downloadGeneticMap
> ### Title: Downloads a genetic map for a particular chromosome under GRCh37
> ###   coordinates for use with sim1000G.
> ### Aliases: downloadGeneticMap
> 
> ### ** Examples
> 
> 
> 
> 
> downloadGeneticMap(22, dir=tempdir() )
 -> Downloading genetic map from: https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr22.txt.gz 
 -> Saving genetic map to:  D:\temp\RtmpWWllqw/genetic_map_GRCh37_chr22.txt.gz 
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in download.file(url, destfile = dest_path, quiet = TRUE) : 
  cannot open URL 'https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr22.txt.gz'
Calls: downloadGeneticMap -> download.file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ExtractingRegionsForSimulation.Rmd' using rmarkdown
Loading required package: hapsim
Loading required package: MASS
Loading required package: stringr
Loading required package: readr
Parsed with column specification:
cols(
  .default = col_character(),
  `#CHROM` = col_double(),
  POS = col_double(),
  QUAL = col_double()
)
See spec(...) for full column specifications.
Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F,  :
  Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
Warning in gplots::heatmap.2(C, col = rev(heat.colors(100)), Rowv = F, Colv = F,  :
  Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
--- finished re-building 'ExtractingRegionsForSimulation.Rmd'

--- re-building 'SimulatingFamilyData.Rmd' using rmarkdown
Loading required package: hapsim
Loading required package: MASS
Loading required package: stringr
Loading required package: readr
Parsed with column specification:
cols(
  .default = col_character(),
  `#CHROM` = col_double(),
  POS = col_double(),
  QUAL = col_double()
)
See spec(...) for full column specifications.
Warning in download.file(url, destfile = dest_path, quiet = TRUE) :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Quitting from lines 68-81 (SimulatingFamilyData.Rmd) 
Error: processing vignette 'SimulatingFamilyData.Rmd' failed with diagnostics:
cannot open URL 'https://github.com/adimitromanolakis/geneticMap-GRCh37/raw/master/genetic_map_GRCh37_chr4.txt.gz'
--- failed re-building 'SimulatingFamilyData.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(simpleCache)
  > 
  > test_check("simpleCache")
  -- 1. Failure: Direct lifespan specification is preferred to background option (
  `t0` not equal to file.info(fp)$ctime.
  1/1 mismatches
  [1] 2020-02-10 14:54:07 - 2020-02-10 14:54:07 == 0.0156 secs
  
  == testthat results  ===========================================================
  [ OK: 66 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Direct lifespan specification is preferred to background option (@test_cache_lifespan.R#123) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'SimRVSequences-Ex.R' failed
The error most likely occurred in:

> ### Name: load_1KG
> ### Title: Load pre-formatted 1000 Genomes Project exon data
> ### Aliases: load_1KG
> 
> ### ** Examples
> 
> exdata = load_1KG(21:22)
Warning in load(url(paste0("https://github.com/simrvprojects/1000-Genomes-Exon-Data/raw/master/Formatted-SNVdata/SNVdata_chrom",  :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in load(url(paste0("https://github.com/simrvprojects/1000-Genomes-Exon-Data/raw/master/Formatted-SNVdata/SNVdata_chrom",  : 
  cannot open the connection
Calls: load_1KG -> load
Execution halted
Error(s) in re-building vignettes:
--- re-building 'SimRVSequences.Rmd' using rmarkdown
Quitting from lines 214-215 (SimRVSequences.Rmd) 
Error: processing vignette 'SimRVSequences.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'SimRVSequences.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.1Mb
Running examples in 'sinew-Ex.R' failed
The error most likely occurred in:

> ### Name: ls_param
> ### Title: Return roxygen2 parameter calls from parameter dictionary
> ### Aliases: ls_param
> 
> ### ** Examples
> 
> repo='https://raw.githubusercontent.com/metrumresearchgroup/sinew/master/'
> dict_loc=file.path(repo,'man-roxygen/Dictionary-1.R')
> ls_param(sinew::makeOxygen,dictionary=dict_loc)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Der Servername oder die Serveradresse konnte nicht verarbeitet werden.'
Error in file(con, "r") : cannot open the connection
Calls: ls_param -> readLines -> file
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.5Mb
Error(s) in re-building vignettes:
--- re-building 'anova-statistics.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'anova-statistics.Rmd'

--- re-building 'bayesian-statistics.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: MASS
Loading required package: Matrix
Loading required package: mvtnorm
Loading required package: sandwich
mediation: Causal Mediation Analysis
Version: 4.5.0

Loading required package: Rcpp
Loading 'brms' package (version 2.11.1). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').
Quitting from lines 62-63 (bayesian-statistics.Rmd) 
Error: processing vignette 'bayesian-statistics.Rmd' failed with diagnostics:
Could not resolve host: raw.githubusercontent.com
--- failed re-building 'bayesian-statistics.Rmd'

--- re-building 'mixedmodels-statistics.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: Matrix
This function will be removed in a future update. There's an enhanced implementation in 'parameters::rescale_weights()' that should be used instead.
--- finished re-building 'mixedmodels-statistics.Rmd'

SUMMARY: processing the following file failed:
  'bayesian-statistics.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'Forecasting.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://raw.githubusercontent.com/christianparobek/skeleSim/master/vignettes/Choosermetasim2.png
HttpExceptionRequest Request {
  host                 = "raw.githubusercontent.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/christianparobek/skeleSim/master/vignettes/Choosermetasim2.png"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
Error: processing vignette 'Forecasting.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'Forecasting.Rmd'

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  slfm_MDN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/slfm.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.6Mb
Warnings in file 'R/replace_special_characters_internal.R':
  unable to translate '<U+00C4>' to native encoding
  unable to translate '<U+00D6>' to native encoding
  unable to translate '<U+00DC>' to native encoding
  unable to translate '<U+00E4>' to native encoding
  unable to translate '<U+00F6>' to native encoding
  unable to translate '<U+00FC>' to native encoding
  unable to translate '<U+00DF>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C6>' to native encoding
  unable to translate '<U+00E6>' to native encoding
  unable to translate '<U+00D8>' to native encoding
  unable to translate '<U+00F8>' to native encoding
  unable to translate '<U+00C5>' to native encoding
  unable to translate '<U+00E5>' to native encoding
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      1.7Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.1Mb
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/4.0/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/4.0/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  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Running 'lint.R' [1s]
  Running 'spelling.R' [0s]
  Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  -- 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  lexical error: invalid char in json text.
                                         NA
                       (right here) ------^
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy_env()
   4. reticulate::conda_list(conda = "auto")
   5. jsonlite::fromJSON(conda_envs)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 50 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   2.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
Running 'testthat.R' [78s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  > test_check("spocc")
  Loading required package: spocc
  -- 1. Failure: occ2df works when eventDate gone - another eg (@test-occ2df.R#44)
  Names of `outdf` ('name', 'longitude', 'latitude', 'prov', 'key') don't match 'name', 'longitude', 'latitude', 'prov', 'key', 'date'
  
  == testthat results  ===========================================================
  [ OK: 100 | SKIPPED: 14 | WARNINGS: 24 | FAILED: 1 ]
  1. Failure: occ2df works when eventDate gone - another eg (@test-occ2df.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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 10.6Mb
  sub-directories of 1Mb or more:
    include   9.4Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    4.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'Details.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: 'gridExtra'

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

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 rows containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggmap'
--- failed re-building 'Details.Rmd'

--- re-building 'Overview.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

To enable 
caching of data, set `options(tigris_use_cache = TRUE)` in your R script or .Rprofile.

Attaching package: 'tigris'

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

    plot

Loading required package: sp
rgeos version: 0.5-2, (SVN revision 621)
 GEOS runtime version: 3.6.1-CAPI-1.10.1 
 Linking to sp version: 1.3-2 
 Polygon checking: TRUE 

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: viridisLite
Warning: Removed 1 rows containing missing values (geom_path).
--- finished re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Package suggested but not available for checking: 'BSgenome.Ptroglodytes.UCSC.panTro5'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Error(s) in re-building vignettes:
--- re-building 'stRvignette.Rmd' using rmarkdown
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
--- failed re-building 'stRvignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/survival.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
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.
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/svmadmm.Rcheck/00install.out' for details.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tesseract.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/testthat.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.00    0.00    2.07 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11483 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.00    0.00    2.09 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11534 (sockconn)
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/tibble.Rcheck/00install.out' for details.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/traitdataform.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   1.5Mb
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  Registered S3 method overwritten by 'trelliscopejs':
    method from   
    +.gg   ggplot2
  > 
  > test_check("trelliscopejs")
  -- 1. Error: examples run without barfing (@test-trelliscope.R#140)  -----------
  Can't cast `data$class2` <cog> to `data$class2` <cog>.
  Backtrace:
    1. base::print(p)
   16. vctrs:::vec_cast.integer.integer(...)
   17. vctrs::vec_default_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   18. vctrs::stop_incompatible_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   19. vctrs:::stop_incompatible(...)
   20. vctrs:::stop_vctrs(...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 695 | FAILED: 1 ]
  1. Error: examples run without barfing (@test-trelliscope.R#140) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
Running 'testthat.R' [47s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tsbox)
  > 
  > test_check("tsbox")
  "blabla"
  -- 1. Error: ts_ based functions pass arguments in seasonal (@test_ts_.R#51)  --
  Process terminated
  Backtrace:
    1. tsbox::ts_seas(ts_c(mdeaths, fdeaths), x11 = "")
    6. tsbox:::fun(.SD, ...)
    7. (function(x, ...) seasonal::final(seasonal::seas(x, ...)))(...)
   10. seasonal::seas(x, ...)
   11. seasonal::checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE)
  
  == testthat results  ===========================================================
  [ OK: 457 | SKIPPED: 13 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ts_ based functions pass arguments in seasonal (@test_ts_.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     6.4Mb
    ubinc   2.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.3Mb
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
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0/uuid.Rcheck/00install.out' for details.
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.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 25.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.3Mb
installed size is 79.1Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     68.8Mb
    proj      5.0Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.3Mb
    htmlwidgets   3.9Mb
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.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  7.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   6.3Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Error(s) in re-building vignettes:
--- re-building 'Running_WhiteStripe.Rmd' using rmarkdown
Quitting from lines 23-26 (Running_WhiteStripe.Rmd) 
Error: processing vignette 'Running_WhiteStripe.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/muschellij2/WhiteStripe/gh-pages/T1Strip.nii.gz'
--- failed re-building 'Running_WhiteStripe.Rmd'

SUMMARY: processing the following file failed:
  'Running_WhiteStripe.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  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
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
Found the following significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0/wrassp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/wrswoR.benchmark.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  -- 1. Failure: opfw - coverage  (@test_opwf.R#69)  -----------------------------
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  == testthat results  ===========================================================
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/x12GUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/x12.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0/x13binary.Rcheck/00install.out' for details.
Running examples in 'x13binary-Ex.R' failed
The error most likely occurred in:

> ### Name: checkX13binary
> ### Title: Check if X-13ARIMA-SEATS Runs Properly
> ### Aliases: checkX13binary
> 
> ### ** Examples
> 
> checkX13binary()
Error in checkX13binary() : X-13 binary file not found
Execution halted
Running 'simpleTest.R' [0s]
Running the tests in 'tests/simpleTest.R' failed.
Complete output:
  > x13binary::checkX13binary()
  Error in x13binary::checkX13binary() : X-13 binary file not found
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0/xml2.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    libs          4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/adaptiveGPCA.Rcheck/00install.out' for details.
Unexported object imported by a ':::' call: 'adehabitatLT:::.ltraj2traj'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  ADAPTgdwm.c:136:73: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/AMORE.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.3Mb
installed size is 73.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.4Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  13.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      2.1Mb
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(assertr)
  > 
  > test_check("assertr")
  -- 1. Failure: assert breaks appropriately (@test-assertions.R#224)  -----------
  `assert(mtcars, in_set(0, 1), vs, tree)` threw an error with unexpected message.
  Expected match: "object 'tree' not found"
  Actual message: "Can't subset columns that don't exist.\nx The column `tree` doesn't exist."
  Backtrace:
    1. testthat::expect_error(...)
   27. vctrs:::stop_subscript_oob(...)
   28. vctrs:::stop_subscript(...)
  
  -- 2. Failure: assert_rows breaks appropriately (@test-assertions.R#290)  ------
  `assert_rows(mtcars, rowSums, in_set(0, 1, 2), vs, am, tree)` threw an error with unexpected message.
  Expected match: "object 'tree' not found"
  Actual message: "Can't subset columns that don't exist.\nx The column `tree` doesn't exist."
  Backtrace:
    1. testthat::expect_error(...)
   27. vctrs:::stop_subscript_oob(...)
   28. vctrs:::stop_subscript(...)
  
  -- 3. Failure: insist breaks appropriately (@test-assertions.R#341)  -----------
  `insist(mtcars, within_n_sds(5), tree)` threw an error with unexpected message.
  Expected match: "object 'tree' not found"
  Actual message: "Can't subset columns that don't exist.\nx The column `tree` doesn't exist."
  Backtrace:
    1. testthat::expect_error(...)
   27. vctrs:::stop_subscript_oob(...)
   28. vctrs:::stop_subscript(...)
  
  == testthat results  ===========================================================
  [ OK: 388 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 3 ]
  1. Failure: assert breaks appropriately (@test-assertions.R#224) 
  2. Failure: assert_rows breaks appropriately (@test-assertions.R#290) 
  3. Failure: insist breaks appropriately (@test-assertions.R#341) 
  
  Error: testthat unit tests failed
  Execution halted
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/4.0gcc8/audio.Rcheck/00install.out' for details.
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2020-01-27 r77730) -- "Unsuffered Consequences"
Copyright (C) 2020 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  7.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   3.3Mb
    libs   2.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Package suggested but not available for checking: 'mzR'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BALD.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bayesCL.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.2Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BcDiag.Rcheck/00install.out' for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 131.9Mb
  sub-directories of 1Mb or more:
    include  130.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.1Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/biganalytics.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.2Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigmemory.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.3Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bigtabulate.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/bioRad.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/BonEV.Rcheck/00install.out' for details.
installed size is 62.4Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      53.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Brundle.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    article   1.9Mb
    libs      2.4Mb
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/4.0gcc8/Cairo.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'lqa'
Running 'testthat.R' [88s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cattonum)
  > 
  > test_check("cattonum")
  -- 1. Failure: conditions work correctly. (@test-conditions.R#7)  --------------
  `catto_label(foo, one_of(x1, x2))` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 254 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: conditions work correctly. (@test-conditions.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [98s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cattonum)
  > 
  > test_check("cattonum")
  -- 1. Failure: conditions work correctly. (@test-conditions.R#7)  --------------
  `catto_label(foo, one_of(x1, x2))` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 254 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: conditions work correctly. (@test-conditions.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    extdata   1.1Mb
    libs      2.2Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   2.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  VCLDefines.c:265:2: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/clv.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.2Mb
    libs      2.0Mb
Package suggested but not available for checking: 'xcms'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.8Mb
CumInt : fn: no visible global function definition for 'integrate'
RND0: no visible global function definition for 'runif'
coxseiInt: no visible global function definition for 'approxfun'
coxseiInt : js: no visible global function definition for 'tail'
coxseiest: no visible global function definition for 'approxfun'
coxseiest : loglik : ll: no visible global function definition for
  'tail'
coxseiest: no visible global function definition for 'optim'
coxseiest2: no visible global function definition for 'approxfun'
coxseiest2: no visible global function definition for 'optim'
coxseiest3: no visible global function definition for 'approxfun'
coxseiest3: no visible global function definition for 'optim'
coxseiexp: no visible global function definition for 'approxfun'
coxseiexp: no visible global function definition for 'optim'
coxseiexp : js: no visible global function definition for 'tail'
coxseiexp: no visible global function definition for 'pnorm'
coxseiexp: no visible global function definition for 'stepfun'
coxseifit.ex: no visible global function definition for 'approxfun'
coxseifit.ex: no visible global function definition for 'optim'
coxseifit.ex : js: no visible global function definition for 'tail'
coxseifit.ex: no visible global function definition for 'pnorm'
coxseifit.ex: no visible global function definition for 'stepfun'
coxseisim : int.at.lasttm: no visible global function definition for
  'tail'
plot.coxsei: no visible global function definition for 'plot'
print.summary.coxsei: no visible global function definition for
  'printCoefmat'
summary.coxsei: no visible global function definition for 'coef'
Undefined global functions or variables:
  approxfun coef integrate optim plot pnorm printCoefmat runif stepfun
  tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "approxfun", "coef", "integrate", "optim", "pnorm",
             "printCoefmat", "runif", "stepfun")
  importFrom("utils", "tail")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cplexAPI.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CSFA.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   4.8Mb
Found the following significant warnings:
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [4294967292, 2147483647] [-Warray-bounds]
  ./src/common/Random.c:105:5: warning: 'memcpy' pointer overflow between offset 0 and size [-4, 9223372036854775807] [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/cubature.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   7.1Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/CVXR.Rcheck/00install.out' for details.
Package required but not available: 'flowDensity'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/RCompile/CRANpkg/lib/4.0gcc8/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   2.4Mb
Found the following significant warnings:
  DTDataFile.cpp:134:19: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'offset' with type 'off_t' {aka 'long int'} [-Warray-bounds]
  DTDataFile.cpp:499:11: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'startOfVariable' with type 'off_t' {aka 'long int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DataGraph.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.1Mb
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:11922 (sockconn)
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv(R_TESTS="")
  > library(testthat)
  > library(DDD)
  > 
  > test_check("DDD")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(descriptr)
  > 
  > test_check("descriptr")
  -- 1. Failure: output from ds_cross_table matches expected results (@test-cross-
  k$row_percent[, 3] not equivalent to c(0.24, 0.48, 0.29).
  1/3 mismatches
  [1] 0.23 - 0.24 == -0.01
  
  == testthat results  ===========================================================
  [ OK: 256 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: output from ds_cross_table matches expected results (@test-cross-table.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Found the following significant warnings:
  clipper.cpp:721:34: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ClipperLib::TEdge'; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: 'strncpy' output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/dggridR.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   4.4Mb
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:11686 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11686 (sockconn)
Execution halted
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:11935 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11935 (sockconn)
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   2.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   2.0Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Warning: declared S3 method 'mean.Distribution' not found
Warning: declared S3 method 'print.ParameterSet' not found
Warning: declared S3 method 'summary.Distribution' not found
Warning: declared S3 method 'median.Distribution' not found
Warning: declared S3 method 'quantile.Distribution' not found
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Running examples in 'distr6-Ex.R' failed
The error most likely occurred in:

> ### Name: Arcsine
> ### Title: Arcsine Distribution Class
> ### Aliases: Arcsine
> 
> ### ** Examples
> 
> x = Arcsine$new(lower = 2, upper = 5)
> 
> # Update parameters
> x$setParameterValue(upper = 4, lower = 1)
> x$parameters()
Error in do.call(get("object")[["print"]], args) : 
  'what' must be a function or character string
Calls: <Anonymous> -> print.R6 -> <Anonymous> -> print -> do.call
Execution halted
Error(s) in re-building vignettes:
--- re-building 'distr6.rmd' using rmarkdown
Quitting from lines 41-44 (distr6.rmd) 
Error: processing vignette 'distr6.rmd' failed with diagnostics:
'what' must be a function or character string
--- failed re-building 'distr6.rmd'

SUMMARY: processing the following file failed:
  'distr6.rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.0Mb
.info: no visible global function definition for 'packageDescription'
redisWorker: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console packageDescription
Consider adding
  importFrom("utils", "flush.console", "packageDescription")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
'::' or ':::' import not declared from: 'ellipsis'
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: colwise mutate gives correct error message if column not found (#
  `mutate_at(tibble(), "test", ~1)` threw an error with unexpected message.
  Expected match: "Unknown column `test`"
  Actual message: "Can't subset columns that don't exist.\nx The column `test` doesn't exist."
  Backtrace:
    1. testthat::expect_error(mutate_at(tibble(), "test", ~1), "Unknown column `test`")
   28. vctrs:::stop_subscript_oob(...)
   29. vctrs:::stop_subscript(...)
  
  == testthat results  ===========================================================
  [ OK: 3617 | SKIPPED: 12 | WARNINGS: 31 | FAILED: 1 ]
  1. Failure: colwise mutate gives correct error message if column not found (#4374) (@test-colwise-mutate.R#430) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: colwise mutate gives correct error message if column not found (#
  `mutate_at(tibble(), "test", ~1)` threw an error with unexpected message.
  Expected match: "Unknown column `test`"
  Actual message: "Can't subset columns that don't exist.\nx The column `test` doesn't exist."
  Backtrace:
    1. testthat::expect_error(mutate_at(tibble(), "test", ~1), "Unknown column `test`")
   28. vctrs:::stop_subscript_oob(...)
   29. vctrs:::stop_subscript(...)
  
  == testthat results  ===========================================================
  [ OK: 3617 | SKIPPED: 12 | WARNINGS: 31 | FAILED: 1 ]
  1. Failure: colwise mutate gives correct error message if column not found (#4374) (@test-colwise-mutate.R#430) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs   5.4Mb
Found the following significant warnings:
  lpkit.h:32:99: warning: right-hand operand of comma expression has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EditImputeCont.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'tidyselect'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.9Mb
Found the following significant warnings:
  emmix.cpp:351:195: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/EMMIXgene.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running examples in 'empiricalFDR.DESeq2-Ex.R' failed
The error most likely occurred in:

> ### Name: empiricalFDR.DESeq2-package
> ### Title: Simulation-Based False Discovery Rate in RNA-Seq
> ### Aliases: empiricalFDR.DESeq2-package empiricalFDR.DESeq2
> 
> ### ** Examples
> 
> 
> dds = makeExampleDESeqDataSet(betaSD=1, n=100)
> dds = DESeq(dds)
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> sims = simulateCounts(dds)
simulating...
================================================================================converting counts to integer mode
> sims = DESeq(sims)
using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> res = results(dds)
Error in .wrap_in_length_one_list_like_object(value, name, x) : 
  failed to coerce 'list(value)' to a DESeqResults object of length 1
Calls: results ... .append_list_element -> .wrap_in_length_one_list_like_object
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eq5d)
  > 
  > test_check("eq5d")
  -- 1. Failure: EQ-5D-3L Iran VAS gives correct answer (@test-eq5d3l.R#266)  ----
  eq5d3l(c(MO = 3, SC = 3, UA = 3, PD = 3, AD = 3), "VAS", "Iran") not equal to -0.07.
  1/1 mismatches
  [1] -0.071 - -0.07 == -0.001
  
  == testthat results  ===========================================================
  [ OK: 402 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: EQ-5D-3L Iran VAS gives correct answer (@test-eq5d3l.R#266) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.1Mb
Running examples in 'fabletools-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.dcmp_ts
> ### Title: Decomposition plots
> ### Aliases: autoplot.dcmp_ts
> 
> ### ** Examples
> 
> if (requireNamespace("feasts", quietly = TRUE)) {
+ library(feasts)
+ library(tsibbledata)
+ aus_production %>% 
+   STL(Beer) %>% 
+   autoplot()
+ }
Error: A model specification is trained to a dataset using the `model()` function.
Refer to the documentation in ?model for more details.
Backtrace:
     x
  1. \-aus_production %>% STL(Beer) %>% autoplot()
  2.   +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3.   \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  4.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  5.       \-`_fseq`(`_lhs`)
  6.         \-magrittr::freduce(value, `_function_list`)
  7.           \-function_list[[i]](value)
  8.             \-feasts::STL(., Beer)
  9.               \-fabletools::new_model_definition(...)
 10.                 +-fabletools:::add_class(.class$new(..., .env = .env), "mdl_defn")
 11.                 \-.class$new(..., .env = .env)
 12.                   \-.subset2(public_bind_env, "initialize")(...)
Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("fabletools")
  Loading required package: fabletools
  Error: A model specification is trained to a dataset using the `model()` function.
  Refer to the documentation in ?model for more details.
  Backtrace:
       x
    1. \-testthat::test_check("fabletools")
    2.   \-testthat:::test_package_dir(...)
    3.     \-testthat::test_dir(...)
    4.       \-testthat::source_test_setup(path, env)
    5.         \-testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    6.           \-base::lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
    7.             \-testthat:::FUN(X[[i]], ...)
    8.               \-base::eval(exprs, env)
    9.                 \-base::eval(exprs, env)
   10.                   \-us_deaths %>% feasts::STL(value) D:\RCompile\CRANpkg\local\4.0gcc8\fabletools.Rcheck\tests\testthat\setup-data.R:30:0
   11.                     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
   12.                     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
   13.                       \-base::eval(quote(`_fseq`(`_lhs
  Execution halted
Aggregation : foo: no visible global function definition for
  'weighted.mean'
Aggregation: no visible global function definition for 'txtProgressBar'
Aggregation: no visible global function definition for
  'setTxtProgressBar'
constructSYB: no visible global function definition for 'str'
fillCountryCode: no visible global function definition for 'na.omit'
getFAO: no visible global function definition for 'read.csv'
getWDImetaData: no visible global function definition for 'write.csv'
getWDItoSYB: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'na.omit'
lsgr: no visible global function definition for 'coef'
lsgr: no visible global function definition for 'lm'
Undefined global functions or variables:
  coef lm na.omit read.csv setTxtProgressBar str txtProgressBar
  weighted.mean write.csv
Consider adding
  importFrom("stats", "coef", "lm", "na.omit", "weighted.mean")
  importFrom("utils", "read.csv", "setTxtProgressBar", "str",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
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/4.0gcc8/FGSG.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'lifeExpectancy.Rmd' using rmarkdown
Quitting from lines 140-156 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
Faceting variables must have at least one value
--- failed re-building 'lifeExpectancy.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   2.2Mb
Package suggested but not available for checking: 'ExtDist'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Package required but not available: 'flowWorkspace'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Found the following significant warnings:
  testcpp_rec6.cpp:197:37: warning: value computed is not used [-Wunused-value]
  testcpp_rec6.cpp:551:37: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/forestFloor.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   6.0Mb
Found the following significant warnings:
  RngStream.c:275:7: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/freeknotsplines.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   3.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   2.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/fs.Rcheck/00install.out' for details.
Found the following significant warnings:
  FunctionalNetworks.c:223:17: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/FunctionalNetworks.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      2.0Mb
PKG_CFLAGS set in 'src/Makevars.in' without any corresponding files
   PKG_CFLAGS set in 'src/Makevars.win' without any corresponding files
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      5.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.9Mb
    proj     5.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.8Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gdns)
  > 
  > test_check("gdns")
  -- 1. Failure: we can do something (@test-gdns.R#4)  ---------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: we can do something (@test-gdns.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R  10.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Running examples in 'GENLIB-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.find.Min.Distance.MRCA
> ### Title: Finds the minimum distances between pairs of individuals given a
> ###   set of ancestors.
> ### Aliases: gen.find.Min.Distance.MRCA
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(geneaJi) 
> genJi<-gen.genealogy(geneaJi) 
> matMRCA<-gen.findMRCA(genJi, individuals=c(1,29), NbProcess = 1)
[1] "warning"
converting NULL pointer to R NULL> gen.find.Min.Distance.MRCA(matMRCA)
Error in gen.find.Min.Distance.MRCA(matMRCA) : 
  genMatrix must be a matrix output from gen.findMRCA
Execution halted
Found the following significant warnings:
  runMCMCfunc.cpp:40:42: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:41:45: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:55:44: warning: left operand of comma operator has no effect [-Wunused-value]
  runMCMCfunc.cpp:56:47: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/geoCount.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Error(s) in re-building vignettes:
--- re-building 'ggBubbles.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 42-57 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'ggBubbles.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Sequence.cpp:387:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:388:17: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Sequence.cpp:387:10: warning: 'char* __builtin_strcpy(char*, const char*)' source argument is the same as destination [-Wrestrict]
  Sequence.cpp:388:10: warning: 'char* __builtin_strcpy(char*, const char*)' source argument is the same as destination [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gkmSVM.Rcheck/00install.out' for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.7Mb
Found the following significant warnings:
  kmppini.cpp:241:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
  kmppini.cpp:275:14: warning: 'void* memcpy(void*, const void*, size_t)' forming offset [5, 8] is out of the bounds [0, 4] of object 'sed' with type 'std::size_t' {aka 'unsigned int'} [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/GMKMcharlie.Rcheck/00install.out' for details.
plot.bGAMM: no visible global function definition for 'par'
plot.bGAMM: no visible global function definition for 'plot'
plot.bGAMM: no visible global function definition for 'lines'
plot.bGAMM: no visible global function definition for 'rug'
Undefined global functions or variables:
  lines par plot rug
Consider adding
  importFrom("graphics", "lines", "par", "plot", "rug")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/gpuR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/haven.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::.__C__GenomicRanges_OR_GenomicRangesList' by 'rtracklayer::.__C__GenomicRanges_OR_GenomicRangesList' when loading 'HiCfeat'
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/HiCfeat.Rcheck/00install.out' for details.
Found the following significant warnings:
  gener.c:39:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  gener.c:39:26: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/hier.part.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.4Mb
Package suggested but not available for checking: 'RGtk2Extras'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   1.8Mb
    libs          3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.0Mb
Package suggested but not available for checking: 'financial'
Found the following significant warnings:
  uuid/gen_uuid.c:321:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/igraph.Rcheck/00install.out' for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
Running 'testthat.R' [191s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(igraph)
  
  Attaching package: 'igraph'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > suppressWarnings(RNGversion("3.5.0"))
  > test_check("igraph")
  -- 1. Failure:  (@test_layout.fr.R#13)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10.8 - 10.8 == 7.97e-05
  
  -- 2. Failure:  (@test_layout.fr.R#22)  ----------------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 941 - 1004 == -62.5
  
  -- 3. Failure: SIR works (@test_sir.R#15)  ---------------------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "bc42d0cbe0bb3321e83979c0432f9cea"
  y[1]: "b73a8ad03b832b3543f2f03d07330398"
  
  == testthat results  =======================================================
  [ OK: 3308 | SKIPPED: 4 | WARNINGS: 1376 | FAILED: 3 ]
  1. Failure:  (@test_layout.fr.R#13) 
  2. Failure:  (@test_layout.fr.R#22) 
  3. Failure: SIR works (@test_sir.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     13.4Mb
Running examples in 'inarmix-Ex.R' failed
The error most likely occurred in:

> ### Name: diagnose
> ### Title: Diagnostics for the model fit.
> ### Aliases: diagnose
> ### Keywords: print
> 
> ### ** Examples
> 
> XX <- cbind(rep(1,9),c(0:8)/4)
> colnames(XX) <- c("const","time")
> coefs <- rbind(c(-.2,0),c(1.2,.3))
> alpha <- c(.2,.2)
> scale <- c(2,2)
> mix.prop <- c(.8,.2)
> 
> testdat <- GenerateMixData(200,coefs,alpha,scale,mix.prop,XX)
> testfit <- inarmix(y~time,nclasses=2,id=subject,data=testdat,maxiter=3)
Iteration:  1 
Iteration:  2 
Iteration:  3 
[1] 8.899245e-157
[1] 8.899245e-157
Error in solve.default(hh$dermat, hh$sqmat) : 
  system is computationally singular: reciprocal condition number = 8.89925e-157
Calls: inarmix -> tcrossprod -> solve -> solve -> solve.default
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'intePareto.Rmd' using rmarkdown
Loading required package: intePareto
get RNA counts
Cache found
get chip counts
use DESeq2 to calculate log2FoldChange of RNA-Seq
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Quitting from lines 118-126 (intePareto.Rmd) 
Error: processing vignette 'intePareto.Rmd' failed with diagnostics:
failed to coerce 'list(value)' to a DESeqResults object of length 1
--- failed re-building 'intePareto.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.3Mb
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:11117 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11117 (sockconn)
Execution halted
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:11398 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11398 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.9Mb
Error(s) in re-building vignettes:
--- re-building 'competing-risks.Rmd' using rmarkdown
Quitting from lines 130-135 (competing-risks.Rmd) 
Error: processing vignette 'competing-risks.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'competing-risks.Rmd'

--- re-building 'joineR.Rmd' using rmarkdown
Quitting from lines 289-300 (joineR.Rmd) 
Error: processing vignette 'joineR.Rmd' failed with diagnostics:
there is no package called 'devtools'
--- failed re-building 'joineR.Rmd'

SUMMARY: processing the following files failed:
  'competing-risks.Rmd' 'joineR.Rmd'

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

> ### Name: add_index.within_participant_mediation
> ### Title: add_index method for within-participant mediation
> ### Aliases: add_index.within_participant_mediation
> 
> ### ** Examples
> 
> ## getting an indirect effect index
> within_model <- mdt_within(data = dohle_siegrist,
+                            IV = name,
+                            DV = willingness,
+                            M = hazardousness,
+                            grouping = participant)
Error: Must extract column with a single subscript.
x The subscript `var` has the wrong type `glue`.
i It must be numeric or character.
Backtrace:
     x
  1. +-JSmediation::mdt_within(...)
  2. \-JSmediation:::mdt_within.data.frame(...)
  3.   +-rlang::is_true(...)
  4.   \-data_long %>% dplyr::pull(DV_cond_1_name) %>% mean()
  5.     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  7.       \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
  8.         \-JSmediation:::`_fseq`(`_lhs`)
  9.           \-magrittr::freduce(value, `_function_list`)
 10.             \-function_list[[i]](value)
 11.               +-dplyr::pull(., DV_cond_1_name)
 12.               \-dplyr:::pull.data.frame(., DV_cond_1_name)
 13.                 \-tidyselect::vars_pull(names(.data), !!enquo(var))
 14.                   \-tidyselect:::pull_as_location2(loc, n, vars)
 15.                     +-tidyselect:::with_subscript_errors(...)
 16.       
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  > 
  > #filter is to disable tests that rely on external servers
  > test_check("jsonlite", filter="toJSON|fromJSON|libjson|serializeJSON")
  Loading required package: jsonlite
  -- 1. Failure: fromJSON Matrix datasets (@test-fromJSON-matrix.R#36)  ----------
  `x` not equal to `expected`.
  6/156 mismatches (average diff: 1e-04)
  [17]  9.19 - 9.19 ==  1e-04
  [23]  9.36 - 9.36 == -1e-04
  [34]  9.69 - 9.69 ==  1e-04
  [65]  4.42 - 4.42 ==  1e-04
  [94]  6.03 - 6.03 == -1e-04
  [108] 6.15 - 6.15 ==  1e-04
  
  == testthat results  ===========================================================
  [ OK: 1473 | SKIPPED: 0 | WARNINGS: 220 | FAILED: 1 ]
  1. Failure: fromJSON Matrix datasets (@test-fromJSON-matrix.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #This file runs all unit tests on every R CMD check.
  > #Comment this out to disable.
  > 
  > library(testthat)
  > 
  > #filter is to disable tests that rely on external servers
  > test_check("jsonlite", filter="toJSON|fromJSON|libjson|serializeJSON")
  Loading required package: jsonlite
  -- 1. Failure: fromJSON Matrix datasets (@test-fromJSON-matrix.R#36)  ----------
  `x` not equal to `expected`.
  6/156 mismatches (average diff: 1e-04)
  [17]  9.19 - 9.19 ==  1e-04
  [23]  9.36 - 9.36 == -1e-04
  [34]  9.69 - 9.69 ==  1e-04
  [65]  4.42 - 4.42 ==  1e-04
  [94]  6.03 - 6.03 == -1e-04
  [108] 6.15 - 6.15 ==  1e-04
  
  == testthat results  ===========================================================
  [ OK: 1473 | SKIPPED: 0 | WARNINGS: 220 | FAILED: 1 ]
  1. Failure: fromJSON Matrix datasets (@test-fromJSON-matrix.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.4Mb
Found the following significant warnings:
  model_simul.cpp:838:22: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  model_simul.cpp:719:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:720:22: warning: '.bin' directive writing 4 bytes into a region of size between 0 and 8 [-Wformat-overflow=]
  model_simul.cpp:721:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:722:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:723:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  model_simul.cpp:724:19: warning: '.bin' directive writing 4 bytes into a region of size between 3 and 11 [-Wformat-overflow=]
  printReadWrite.cpp:54:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:74:23: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:84:25: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:138:38: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:139:40: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:140:47: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:141:45: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
  printReadWrite.cpp:152:91: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/landsepi.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  69.5Mb
    proj   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    help   1.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.6Mb
Found the following significant warnings:

  Warning: 'indexClass<-' is deprecated.
  Warning: 'indexClass<-' is deprecated.
  Warning: 'indexClass<-' is deprecated.
  Warning: 'indexClass<-' is deprecated.
  Warning: 'indexClass<-' is deprecated.
  Warning: 'indexClass<-' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      3.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   2.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    doc        2.4Mb
    libs       2.6Mb
    testdata   1.6Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: 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/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: 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/4.0gcc8/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: 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/4.0gcc8/lolog.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      2.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.1Mb
    libs   2.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    libs   2.1Mb
Found the following significant warnings:
  liblwgeom/lwgeom_topo.c:4485:36: warning: too many arguments for format [-Wformat-extra-args]
  liblwgeom/lwgeom_topo.c:4536:38: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/lwgeom.Rcheck/00install.out' for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
    proj   5.0Mb
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/4.0gcc8/lxb.Rcheck/00install.out' for details.
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.8Mb
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ManifoldOptim.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          8.3Mb
Found the following significant warnings:
  cuts.c:24:2: warning: statement with no effect [-Wunused-value]
  cuts.c:24:5: warning: statement with no effect [-Wunused-value]
  cuts.c:24:9: warning: statement with no effect [-Wunused-value]
  cuts.c:32:2: warning: statement with no effect [-Wunused-value]
  cuts.c:32:6: warning: statement with no effect [-Wunused-value]
  cuts.c:32:10: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mapproj.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   3.2Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "dsparseModelMatrix": order chosen is inconsistent with the superclasses of "sparseModelMatrix"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MatrixModels.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      2.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.6Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  -- 1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202)  --------
  package or namespace load failed for 'phyloseq' in library.dynam(lib, package, package.lib):
   DLL 'Rhdf5lib' not found: maybe not installed for this architecture?
  Backtrace:
   1. base::library(phyloseq)
   2. base::tryCatch(...)
   3. base:::tryCatchList(expr, classes, parentenv, handlers)
   4. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5. value[[3L]](cond)
  
  == testthat results  ===========================================================
  [ OK: 95 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Converting to phyloseq (@test--parsers_and_writers.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'MetaIntegrator.Rmd' using rmarkdown
Quitting from lines 128-129 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'MetaIntegrator.Rmd'

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs   4.5Mb
    misc   1.1Mb
.snqProfitImposeConvexityStEr: no visible global function definition
  for 'runif'
predict.snqProfitEst: no visible global function definition for
  'model.matrix'
predict.snqProfitEst: no visible global function definition for 'qt'
predict.snqProfitEst: no visible global function definition for
  'df.residual'
predict.snqProfitEst: no visible global function definition for
  'residuals'
snqProfitCoef: no visible global function definition for 'pt'
snqProfitEla: no visible global function definition for 'pt'
snqProfitEst: no visible global function definition for 'as.formula'
snqProfitEst: no visible global function definition for 'coef'
snqProfitEst: no visible global function definition for 'vcov'
snqProfitEst: no visible global function definition for 'fitted'
snqProfitEst: no visible global function definition for 'df.residual'
snqProfitImposeConvexity: no visible global function definition for
  'optim'
snqProfitSystem: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula coef df.residual fitted model.matrix optim pt qt residuals
  runif vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "df.residual", "fitted",
             "model.matrix", "optim", "pt", "qt", "residuals", "runif",
             "vcov")
to your NAMESPACE file.
Found the following significant warnings:
  migrate.c:180:30: warning: '%d' directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:187:26: warning: '.asc' directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:200:28: warning: '.asc' directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:287:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:313:29: warning: '%d' directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:560:31: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:596:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:604:27: warning: '%s' directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/MigClim.Rcheck/00install.out' for details.
Found the following significant warnings:
  GLMM_Deviance.cpp:153:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance.cpp:708:11: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:173:9: warning: statement has no effect [-Wunused-value]
  GLMM_Deviance2.cpp:780:11: warning: statement has no effect [-Wunused-value]
  GLMM_newData.cpp:183:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:161:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf.cpp:626:11: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:124:9: warning: statement has no effect [-Wunused-value]
  GLMM_updateRanEf_QR.cpp:328:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:104:11: warning: statement has no effect [-Wunused-value]
  MCMC_Moments_NormalApprox_QR.cpp:209:11: warning: statement has no effect [-Wunused-value]
  NMix_updateMeansVars.cpp:516:16: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixAK.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mixKernel.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   2.5Mb
Found the following significant warnings:
  ./bson/bson-macros.h:180:19: warning: ISO C does not support '__FUNCTION__' predefined identifier [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/mongolite.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.6Mb
    libs   1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.2Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  21.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Found the following significant warnings:
  eclat/tract/src/tract.c:1399:41: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/multinet.Rcheck/00install.out' for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
    libs   2.0Mb
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 'd:/Rcompile/CRANpkg/local/4.0gcc8/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.6Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.2Mb
    include   5.6Mb
    libs      2.4Mb
    tests     1.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs   3.3Mb
Error(s) in re-building vignettes:
--- re-building 'NutrienTrackeR.Rmd' using rmarkdown
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 146-147 (NutrienTrackeR.Rmd) 
Error: processing vignette 'NutrienTrackeR.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'NutrienTrackeR.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.5Mb
    libs   2.5Mb
PKG_CFLAGS set in 'src/Makevars.in' without any corresponding files
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
Running examples in 'opencastR-Ex.R' failed
The error most likely occurred in:

> ### Name: oc_group
> ### Title: Query Opencast for a specific group
> ### Aliases: oc_group
> 
> ### ** Examples
> 
> Sys.setenv(OPENCAST_HOST = "https://legacy.opencast.org")
> Sys.setenv(OPENCAST_USERNAME = "admin")
> Sys.setenv(OPENCAST_PASSWORD = "opencast")
> 
> oc_group("MH_DEFAULT_ORG_EXTERNAL_APPLICATIONS")
Error: lexical error: invalid char in json text.
                                       Cannot find a group with id 'MH
                     (right here) ------^
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/OpenCL.Rcheck/00install.out' for details.
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    libs   19.8Mb
    share   9.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.7Mb
    models   4.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.3Mb
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/opusminer.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.6Mb
Found the following significant warnings:
  likelihoods.cpp:479:38: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/outbreaker2.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    doc    1.3Mb
    libs   2.0Mb
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/4.0gcc8/pbdRPC.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  13.9Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs   13.8Mb
    share  11.9Mb
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:11763 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11763 (sockconn)
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs        2.0Mb
    xvg-files   3.2Mb
Found the following significant warnings:
  permTest.c:20:3: warning: statement with no effect [-Wunused-value]
  permTest.c:62:3: warning: statement with no effect [-Wunused-value]
  permTest.c:90:3: warning: statement with no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/permDep.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phateR.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      2.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/phyloseqGraphTest.Rcheck/00install.out' for details.
Warning in inla.print.version() :
  INLA_18.07.12: 32bit binaries are no longer supported!

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    3.0Mb
Error(s) in re-building vignettes:
--- re-building 'Overview.Rmd' using rmarkdown
Quitting from lines 547-548 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'magick'
--- failed re-building 'Overview.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.6Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/PPRL.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'introduction_to_prcr.Rmd' using rmarkdown
################################
Clustering data for iteration 2
Clustering data for iteration 3
Clustering data for iteration 4
################################
################################
################################
Clustering data for iteration 1

Could not calculate agreement because k-means algorithm did not converge
Clustering data for iteration 2
Quitting from lines 62-70 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
Can't subset columns that don't exist.
x The columns `1`, `1`, `1`, `2`, `2`, etc. don't exist.
--- failed re-building 'introduction_to_prcr.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.1Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
    proj   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.3Mb
    libs   3.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.6Mb
Error(s) in re-building vignettes:
--- re-building 'Critical-distances.Rmd' using rmarkdown
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/Quartet.Rch
eck/vign_test/Quartet/vignettes/Critical-distances_files/figure-latex/Plot\%20t
rees-1.pdf' not found.

Error: processing vignette 'Critical-distances.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/Quartet.Rcheck/vign_test/Quartet/vignettes/Critical-distances.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Critical-distances.log for more info.
--- failed re-building 'Critical-distances.Rmd'

--- re-building 'Tree-distance-metrics.Rmd' using rmarkdown
Warning: Package amsmath Warning: Foreign command \atopwithdelims;
(amsmath)                \frac or \genfrac should be used instead
(amsmath)                 on input line 149.
--- finished re-building 'Tree-distance-metrics.Rmd'

SUMMARY: processing the following file failed:
  'Critical-distances.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin     12.3Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   2.1Mb
cpc_get_rawdata: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    help   1.2Mb
    libs   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.0Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.8Mb
Found the following significant warnings:
  avc_binwr.c:166:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: 'strncpy' output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: '%4.4d' directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: '%s' directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: 'sprintf' may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: '-ID' directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: '%s' directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: '%s' directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: '%s' directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RArcInfo.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   4.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rblpapi.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rcplex.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.1Mb
    libs      2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      2.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      3.4Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      2.3Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib      13.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.5Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RcppXsimd)
  > 
  > test_check("RcppXsimd")
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcrypt)
  > 
  > test_check("rcrypt")
  gpg: decryption failed: bad key
  -- 1. Error: Decryption with passphrase passthrough and armor works (@test-decry
  cannot open the connection
  Backtrace:
   1. base::readLines("file2-decrypt.txt")
   2. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 18 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: Decryption with passphrase passthrough and armor works (@test-decrypt.r#69) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  -- 1. Failure: csf algorithm works (@test-CSF.R#8)  ----------------------------
  length(id_ground) not equal to `expected`.
  1/1 mismatches
  [1] 15459 - 15453 == 6
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: csf algorithm works (@test-CSF.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: 'strncpy' output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: 'strncpy' output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rdsdp.Rcheck/00install.out' for details.
Found the following significant warnings:
  compile.cc:292:69: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class re2::Prog::Inst'; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: 'void* memmove(void*, const void*, size_t)' writing to an object of type 'class re2::Regexp' with no trivial copy-assignment [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/re2r.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      69.2Mb
    pictures   1.3Mb
    proj       5.0Mb
Found the following significant warnings:
  IP2Location.c:339:35: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:893:39: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
  IP2Location.c:900:41: warning: passing argument 3 of 'inet_pton' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rgeolocate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      2.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    1.4Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
Found the following significant warnings:
  fakemaster.c:82:57: warning: embedded '\0' in format [-Wformat-contains-nul]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/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/4.0gcc8/RInside.Rcheck/00install.out' for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    lib    6.3Mb
    libs   8.0Mb
Found the following significant warnings:
  Rinit.c:251:21: warning: assignment to 'blah1' {aka 'int (*)(const char *, char *, int,  int)'} from incompatible pointer type 'int (*)(const char *, unsigned char *, int,  int)' [-Wincompatible-pointer-types]
  Rinit.c:257:21: warning: assignment to 'blah5' {aka 'int (*)(const char *)'} from incompatible pointer type 'int (*)(char *)' [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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 'sink.R' [0s]
  Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Workaround for loadNamespace() failure on R 3.2
  > requireNamespace("rlang")
  Loading required namespace: rlang
  > 
  > library("testthat")
  > library("rlang")
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > 
  > test_check("rlang")
  -- 1. Failure: operands are wrapped in parentheses to ensure correct predecence 
  `object` not identical to `expected`.
  1/1 mismatches
  x[1]: "(function() 1) ? 2"
  y[1]: "function() 1 ? 2"
  
  w finalized
  == testthat results  ===========================================================
  [ OK: 2592 | SKIPPED: 38 | WARNINGS: 13 | FAILED: 1 ]
  1. Failure: operands are wrapped in parentheses to ensure correct predecence (@test-deparse.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'sink.R' [0s]
  Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Workaround for loadNamespace() failure on R 3.2
  > requireNamespace("rlang")
  Loading required namespace: rlang
  > 
  > library("testthat")
  > library("rlang")
  
  Attaching package: 'rlang'
  
  The following objects are masked from 'package:testthat':
  
      is_false, is_null, is_true
  
  > 
  > test_check("rlang")
  -- 1. Failure: operands are wrapped in parentheses to ensure correct predecence 
  `object` not identical to `expected`.
  1/1 mismatches
  x[1]: "(function() 1) ? 2"
  y[1]: "function() 1 ? 2"
  
  w finalized
  == testthat results  ===========================================================
  [ OK: 2592 | SKIPPED: 38 | WARNINGS: 13 | FAILED: 1 ]
  1. Failure: operands are wrapped in parentheses to ensure correct predecence (@test-deparse.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rmagic.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   2.8Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type 'class NxsException' by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type 'class NxsException' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rncl.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'test-all.R' [256s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  -- 1. Error: We can extract tree and trait data to run fitContinuous and fitDisc
  Unknown states 0 not allowed in states vector
  Backtrace:
   1. geiger::fitDiscrete(tree, traits[2], ncores = 1)
   2. geiger::mkn.lik(...)
   3. geiger:::.make.cache.mkn(...)
   4. geiger:::.check.states(tree, states, strict.vals = 1:k)
  
  Namespace prefix xhtml on div is not defined
  Done simulation(s).
  == testthat results  ===========================================================
  [ OK: 626 | SKIPPED: 2 | WARNINGS: 7 | FAILED: 1 ]
  1. Error: We can extract tree and trait data to run fitContinuous and fitDiscrete (@test_comp_analysis.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'S4.Rmd' using rmarkdown
Loading required package: ape
--- finished re-building 'S4.Rmd'

--- re-building 'intro.Rmd' using rmarkdown
Quitting from lines 164-167 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Unknown states 0 not allowed in states vector
--- failed re-building 'intro.Rmd'

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

--- re-building 'simmap.Rmd' using rmarkdown
Loading required package: maps
--- finished re-building 'simmap.Rmd'

--- re-building 'sparql.Rmd' using rmarkdown
Loading required package: ape
Loading required package: maps
--- finished re-building 'sparql.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:
    doxygen   1.4Mb
    libs      2.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.5Mb
Found the following significant warnings:
  Warning: unable to find a consistent ordering of superclasses for class "GPDORobEstimate": order chosen is inconsistent with the superclasses of "GPDkStepEstimate"
  Warning: unable to find a consistent ordering of superclasses for class "GEVORobEstimate": order chosen is inconsistent with the superclasses of "GEVkStepEstimate"
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RobExtremes.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/ROracle.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.7Mb
Found the following significant warnings:
  bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:241:31: warning: ', ' directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rphast.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
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:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.4Mb
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Found the following significant warnings:

  Warning: 'ph_with_vg_at' is deprecated.
  Warning: 'ph_with_vg_at' is deprecated.
  Warning: 'ph_with_vg_at' is deprecated.
  Warning: 'ph_with_vg_at' is deprecated.
  Warning: 'ph_with_vg_at' is deprecated.
  Warning: 'ph_with_vg_at' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error(s) in re-building vignettes:
--- re-building 'rscala.Rnw' using Sweave
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB


Error: processing vignette 'rscala.Rnw' failed with diagnostics:
 chunk 7 (label = Instantiate a bridge for this document) 
Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>



--- failed re-building 'rscala.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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/4.0gcc8/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/4.0gcc8/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/4.0gcc8/Rserve/libs/i386/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 'd:/Rcompile/CRANpkg/lib/4.0gcc8/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/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
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 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  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/4.0gcc8/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:  3.83 0.18 4.02 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  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstanarm.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstap.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
Found the following significant warnings:
  RngStreams.c:332:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/rstream.Rcheck/00install.out' for details.
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) (2020-01-27 r77730)
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_4.0.0
> 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  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
Found the following significant warnings:
  vcglib/wrap/ply/plylib.cpp:3666:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rvcg.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following sources/headers with CR or CRLF line endings:
  src/vcglib/wrap/nanoply/include/nanoplyWrapper.hpp
Some Unix compilers require LF line endings.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.8Mb
Error(s) in re-building vignettes:
--- re-building 'rxnat.Rmd' using rmarkdown
Quitting from lines 98-100 (rxnat.Rmd) 
Error: processing vignette 'rxnat.Rmd' failed with diagnostics:
error during HTTP request
--- failed re-building 'rxnat.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata   1.3Mb
    libs      2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   2.0Mb
Package suggested but not available for checking: 'loomR'
Package unavailable to check Rd xrefs: 'loomR'
installed size is 95.5Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.6Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SigTree.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.1Mb
Missing link or links in documentation object 'tidy_labels.Rd':
  '[sjPlot]{sjp.xtab}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  slfm_MDN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/slfm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/smapr.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Running 'testthat.R' [92s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.7 loaded.
  This is package "smooth", v2.5.4
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  createPosDef.cpp:84:13: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/smoothSurv.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.8Mb
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/4.0gcc8/SongEvo.Rch
eck/vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20populatio
n\%20size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/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
Package suggested but not available for checking: 'SciencesPo'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   2.8Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   3.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   3.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: 'strncpy' output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: 'strncpy' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: 'strncpy' output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SSN.Rcheck/00install.out' for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    include   9.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/stepwise.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/strum.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/superbiclust.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   2.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/svmadmm.Rcheck/00install.out' for details.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Error(s) in re-building vignettes:
--- re-building 'tealeaves-intermediate.Rmd' using rmarkdown
--- finished re-building 'tealeaves-intermediate.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpKIfvUN\file1170c7a3a3aa7': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.9Mb
    tessdata  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0gcc8/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair<const std::pair<unsigned int, unsigned int>, int>'; use 'new' and 'delete' instead [-Wclass-memaccess]
  D:/RCompile/CRANpkg/lib/4.0gcc8/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: 'void* realloc(void*, size_t)' moving an object of non-trivially copyable type 'struct std::pair<const std::pair<unsigned int, unsigned int>, float>'; use 'new' and 'delete' instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/text2vec.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.6Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.01    0.00    2.93 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11659 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.00    0.00    2.53 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11709 (sockconn)
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/theseus.Rcheck/00install.out' for details.
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tibbleOne)
  > 
  > test_check("tibbleOne")
  -- 1. Error: correct inputs work (@test-to_kable.R#38)  ------------------------
  Names must be unique.
  Backtrace:
    1. tibbleOne::to_kable(tb1, format = "latex")
    2. [ `%<>%`(...) ] with 7 more calls
   11. dplyr:::rename.data.frame(., !!!names_to_repair)
   12. tidyselect::vars_rename(names(.data), !!!enquos(...))
   13. tidyselect:::rename_impl(NULL, .vars, quo(c(...)), strict = .strict)
   21. vctrs::vec_as_names(names, repair = "check_unique")
   22. vctrs:::validate_unique(names)
   23. vctrs:::stop_names_must_be_unique(which(duplicated(names)))
   24. vctrs:::stop_names(...)
   25. vctrs:::stop_vctrs(...)
  
  == testthat results  ===========================================================
  [ OK: 36 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 1 ]
  1. Error: correct inputs work (@test-to_kable.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [109s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This is necessary because some tests fail otherwise; see https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(tidybayes)
  > 
  > test_check("tidybayes")
  -- 1. Failure: [add_]predicted_draws works on brms models with categorical outco
  predicted_draws(m_cyl_mpg, mtcars_tbl, seed = 1234, n = 100) not equal to `ref`.
  Incompatible type for column `.prediction`: x numeric, y factor
  
  -- 2. Failure: [add_]predicted_draws works on brms models with categorical outco
  add_predicted_draws(mtcars_tbl, m_cyl_mpg, seed = 1234, n = 100) not equal to `ref`.
  Incompatible type for column `.prediction`: x numeric, y factor
  
  == testthat results  ===========================================================
  [ OK: 271 | SKIPPED: 41 | WARNINGS: 38 | FAILED: 2 ]
  1. Failure: [add_]predicted_draws works on brms models with categorical outcomes (@test.predicted_draws.R#126) 
  2. Failure: [add_]predicted_draws works on brms models with categorical outcomes (@test.predicted_draws.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
Package vignette with placeholder title 'Vignette Title':
  'tidyrules_vignette.Rmd'
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    examples  19.5Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/treeDA.Rcheck/00install.out' for details.
Running examples in 'tree.interpreter-Ex.R' failed
The error most likely occurred in:

> ### Name: MDITree
> ### Title: Mean Decrease in Impurity
> ### Aliases: MDITree MDI
> 
> ### ** Examples
> 
> library(ranger)
> rfobj <- ranger(Species ~ ., iris, keep.inbag=TRUE)
> tidy.RF <- tidyRF(rfobj, iris[, -5], iris[, 5])
> MDITree(tidy.RF, 1, iris[, -5], iris[, 5])

error: Cube::subcube(): indices out of bounds or incorrectly used
Error in featureContribTreeCpp(tidy.RF, tree - 1, X) : 
  Cube::subcube(): indices out of bounds or incorrectly used
Calls: MDITree -> featureContribTree -> featureContribTreeCpp
Execution halted
Running examples in 'tree.interpreter-Ex.R' failed
The error most likely occurred in:

> ### Name: MDITree
> ### Title: Mean Decrease in Impurity
> ### Aliases: MDITree MDI
> 
> ### ** Examples
> 
> library(ranger)
> rfobj <- ranger(Species ~ ., iris, keep.inbag=TRUE)
> tidy.RF <- tidyRF(rfobj, iris[, -5], iris[, 5])
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tree.interpreter)
  > 
  > test_check("tree.interpreter")
Error(s) in re-building vignettes:
--- re-building 'MDI.Rmd' using rmarkdown
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   2.0Mb
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  Registered S3 method overwritten by 'trelliscopejs':
    method from   
    +.gg   ggplot2
  > 
  > test_check("trelliscopejs")
  -- 1. Error: examples run without barfing (@test-trelliscope.R#140)  -----------
  Can't cast `data$class2` <cog> to `data$class2` <cog>.
  Backtrace:
    1. base::print(p)
   16. vctrs:::vec_cast.integer.integer(...)
   17. vctrs::vec_default_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   18. vctrs::stop_incompatible_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   19. vctrs:::stop_incompatible(...)
   20. vctrs:::stop_vctrs(...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 695 | FAILED: 1 ]
  1. Error: examples run without barfing (@test-trelliscope.R#140) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  12.0Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(rlang)
  > library(tibble)
  > library(lubridate)
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:rlang':
  
      is_false, is_null, is_true
  
  > library(tsibble)
  
  Attaching package: 'tsibble'
  
  The following objects are masked from 'package:lubridate':
  
      interval, new_interval
  
  > 
  > set.seed(2018)
  > test_check("tsibble")
  -- 1. Failure: a tbl_ts of 4 day interval with bad names (@test-gaps.R#74)  ----
  `fill_gaps(tsbl, value1 = value)` threw an error with unexpected message.
  Expected match: "Unknown column"
  Actual message: "Can't subset columns that don't exist.\nx The column `value1` doesn't exist."
  Backtrace:
    1. testthat::expect_error(fill_gaps(tsbl, value1 = value), "Unknown column")
   26. vctrs:::stop_subscript_oob(...)
   27. vctrs:::stop_subscript(...)
  
  == testthat results  ===========================================================
  [ OK: 789 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: a tbl_ts of 4 day interval with bad names (@test-gaps.R#74) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: 'strncat' output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/TukeyRegion.Rcheck/00install.out' for details.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    libs   2.9Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(usefun)
  > 
  > test_check("usefun")
  -- 1. Failure: it returns proper results (@test-others.R#33)  ------------------
  specify_decimal(number = 0.12345, digits.to.keep = 4) not equal to "0.1234".
  1/1 mismatches
  x[1]: "0.1235"
  y[1]: "0.1234"
  
  == testthat results  ===========================================================
  [ OK: 110 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: it returns proper results (@test-others.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/uuid.Rcheck/00install.out' for details.
installed size is 25.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  23.2Mb
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<> >::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<> >' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member' {aka 'struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>'} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/validatejsonr.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.4Mb
    proj      5.0Mb
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:ranger':

    importance

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

    margin

Loading required package: parallel
Quitting from lines 347-378 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
object 'epi' not found
--- failed re-building 'varrank.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.7Mb
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: variantSetEnrichment
> ### Aliases: variantSetEnrichment
> ### Keywords: VSE
> 
> ### ** Examples
> 
> ## Not run: 
> ##D variantSetEnrichment(avs, mrvs, regions=samples)
> ##D #We have included the output from our example analysis with the package. \
> ##D You can load the example VariantSetEnrichment output by typing:
> ##D load(file.path(system.file("extdata", "vse_output.Rda", package="VSE")))
> ## End(Not run)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  31.4 0.58 32.4 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  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plo
t-1.pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rchec
k/vign_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20
rho-1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile D:/RCompile/CRANpkg/local/4.0gcc8/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.2Mb
Found the following significant warnings:
  tabix/razf.c:188:2: warning: 'strncpy' output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/WhopGenome.Rcheck/00install.out' for details.
Found the following significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/wrassp.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/x13binary.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XML.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    libs          4.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      2.1Mb
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/yaml.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Dependence on R version ‘3.4.2’ not with patchlevel 0
Found the following significant warnings:
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/circglmbayes.Rcheck/00install.out’ for details.
makeX_eset: no visible global function definition for ‘model.matrix’
normFit: no visible binding for global variable ‘lm’
normFit: no visible binding for global variable ‘sd’
normFit: no visible global function definition for ‘lm’
normPred: no visible binding for global variable ‘predict’
normPred: no visible global function definition for ‘predict’
normPred: no visible binding for global variable ‘median’
plot.nFit: no visible global function definition for ‘par’
plot.nFit: no visible global function definition for ‘barplot’
plot.nFit: no visible global function definition for ‘legend’
show_nfit: no visible global function definition for ‘anova’
show_nfit: no visible global function definition for ‘residuals’
show_nfit: no visible global function definition for ‘fitted’
standardsFit: no visible binding for global variable ‘lm’
standardsFit: no visible global function definition for ‘resid’
standardsFit: no visible global function definition for
  ‘compareVersion’
standardsPred: no visible global function definition for ‘predict’
makeX,ExpressionSet-character: no visible global function definition
  for ‘model.matrix’
plot,nFit: no visible global function definition for ‘par’
plot,nFit: no visible global function definition for ‘barplot’
plot,nFit: no visible global function definition for ‘legend’
show,nFit: no visible global function definition for ‘anova’
show,nFit: no visible global function definition for ‘residuals’
show,nFit: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
Documented arguments not in \usage in documentation object 'Subtotal-class':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pcaL1’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DistributionOptimization.Rcheck/00install.out’ for details.
Documented arguments not in \usage in documentation object 'eqnlist':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [4s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  ── 1. Failure: Countrycodes use eurostat for missing (@test-all.R#105)  ────────
  suppressWarnings(...) not equal to c("Finland", "Germany", "European Union - 28 countries").
  1/3 mismatches
  x[3]: "European Union - 28 countries (2013-2020)"
  y[3]: "European Union - 28 countries"
  
  trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Froad_pa_buscoa.tsv.gz'
  Content type 'application/octet-stream;charset=UTF-8' length 5176 bytes
  ==================================================
  downloaded 5176 bytes
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 20 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Countrycodes use eurostat for missing (@test-all.R#105) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘ExtDist’
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘geoRglm’
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

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

    fortify

Killed
Documented arguments not in \usage in documentation object 'dReport':
  ‘....’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘bayesSurv’
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(itunesr)
  > 
  > test_check("itunesr")
  ── 1. Error: The output dataframe Type is  (@test-fun.R#7)  ────────────────────
  attempt to set an attribute on NULL
  Backtrace:
   1. testthat::expect_equal(...)
   4. itunesr::getReviews("297606951", "in", 2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: The output dataframe Type is  (@test-fun.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Dependence on R version ‘3.4.4’ not with patchlevel 0
Documented arguments not in \usage in documentation object 'kde.truncate':
  ‘...’

Documented arguments not in \usage in documentation object 'kdr':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘lbfgsb3c.Rmd’ using rmarkdown
Quitting from lines 139-237 (lbfgsb3c.Rmd) 
Error: processing vignette 'lbfgsb3c.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘lbfgsb3c.Rmd’

SUMMARY: processing the following file failed:
  ‘lbfgsb3c.Rmd’

Error: Vignette re-building failed.
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:182:19: 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:896:16: 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:196:19: 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 ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
Dependence on R version ‘3.4.3’ not with patchlevel 0
Found the following significant warnings:
  migrate.c:180:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:187:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:200:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:287:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:313:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:560:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:596:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:604:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(con_pre,ex_pre,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 01")   
     orddom_f(con_post,ex_post,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 02") 
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [20s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pcts)
  Loading required package: sarima
  Loading required package: FitAR
  Loading required package: lattice
  Loading required package: leaps
  Loading required package: ltsa
  Loading required package: bestglm
  Loading required package: stats4
  > 
  > test_check("pcts")
  ── 1. Failure: pclsdf works correctly (@test-pclsdf.R#27)  ─────────────────────
  `res` has changed from known value recorded in 'pclsdf_FTFF.rds'.
  Component "sslope": names for target but not for current
  Component "sslope": Numeric: lengths (4, 0) differ
  
  ── 2. Failure: pclsdf works correctly (@test-pclsdf.R#27)  ─────────────────────
  `res` has changed from known value recorded in 'pclsdf_FTFT.rds'.
  Component "sslope": names for target but not for current
  Component "sslope": Numeric: lengths (4, 0) differ
  
  ── 3. Failure: pclsdf works correctly (@test-pclsdf.R#27)  ─────────────────────
  `res` has changed from known value recorded in 'pclsdf_FTTF.rds'.
  Component "sslope": names for target but not for current
  Component "sslope": Numeric: lengths (4, 0) differ
  
  ── 4. Failure: pclsdf works correctly (@test-pclsdf.R#27)  ─────────────────────
  `res` has changed from known value recorded in 'pclsdf_FTTT.rds'.
  Component "sslope": names for target but not for current
  Component "sslope": Numeric: lengths (4, 0) differ
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 155 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: pclsdf works correctly (@test-pclsdf.R#27) 
  2. Failure: pclsdf works correctly (@test-pclsdf.R#27) 
  3. Failure: pclsdf works correctly (@test-pclsdf.R#27) 
  4. Failure: pclsdf works correctly (@test-pclsdf.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Documented arguments not in \usage in documentation object 'performance_score':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘artificial_intelligence_evolution.Rmd’ using rmarkdown
Quitting from lines 21-35 (artificial_intelligence_evolution.Rmd) 
Error: processing vignette 'artificial_intelligence_evolution.Rmd' failed with diagnostics:
GnuTLS recv error (-54): Error in the pull function.
--- failed re-building ‘artificial_intelligence_evolution.Rmd’

--- re-building ‘gas_influx_overbalanced.Rmd’ using rmarkdown
Quitting from lines 44-61 (gas_influx_overbalanced.Rmd) 
Error: processing vignette 'gas_influx_overbalanced.Rmd' failed with diagnostics:
GnuTLS recv error (-54): Error in the pull function.
--- failed re-building ‘gas_influx_overbalanced.Rmd’

--- re-building ‘gas_lift_keywords_variation.Rmd’ using rmarkdown
Quitting from lines 58-70 (gas_lift_keywords_variation.Rmd) 
Error: processing vignette 'gas_lift_keywords_variation.Rmd' failed with diagnostics:
GnuTLS recv error (-54): Error in the pull function.
--- failed re-building ‘gas_lift_keywords_variation.Rmd’

SUMMARY: processing the following files failed:
  ‘artificial_intelligence_evolution.Rmd’ ‘gas_influx_overbalanced.Rmd’
  ‘gas_lift_keywords_variation.Rmd’

Error: Vignette re-building failed.
Execution halted
Unknown package ‘RecordLinkage’ in Rd xrefs
Documented arguments not in \usage in documentation object 'equivalent_shifts':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘test-async.R’ [15s/19s]
  Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/test-async.R’ failed.
Complete output:
  > 
  > if (file.exists("async")) {
  +   library(testthat)
  +   library(pkgcache)
  +   test <- function() {
  +     package <- "pkgcache"
  +     env_test <- asNamespace("testthat")$env_test
  +     env_test$in_test <- TRUE
  +     env_test$package <- package
  +     on.exit({
  +       env_test$in_test <- FALSE
  +       env_test$package <- NULL
  +     })
  +     test_path <- "async"
  +     asNamespace("testthat")$test_package_dir(
  +       package = package, test_path = test_path,
  +       filter = NULL, reporter = "check")
  +   }
  +   test()
  + }
  ── 1. Failure: when_any, multiple errors (@test-when-any.R#73)  ────────────────
  conditionMessage\(errors\[\[1\]\]\) does not match "bar".
  Actual value: "foo"
  
  ── 2. Failure: when_any, multiple errors (@test-when-any.R#74)  ────────────────
  conditionMessage\(errors\[\[2\]\]\) does not match "foo".
  Actual value: "bar"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 661 | SKIPPED: 31 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: when_any, multiple errors (@test-when-any.R#73) 
  2. Failure: when_any, multiple errors (@test-when-any.R#74) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [81s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PlackettLuce)
  > 
  > test_check("PlackettLuce")
  ── 1. Error: (unknown) (@test-log-likelihood.R#81)  ────────────────────────────
  The package Matrix.utils is needed for this function to work. Please install it.
  Backtrace:
   1. BradleyTerryScalable::btdata(as.data.frame(cbind(M, 1)))
   2. BradleyTerryScalable:::pairs_to_matrix(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 168 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-log-likelihood.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [151s/148s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  ── 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ─────────
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1390 | SKIPPED: 43 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: ‘trelliscopejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABE.Rmd’ using rmarkdown
--- finished re-building ‘ABE.Rmd’

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

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

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

--- re-building ‘RSABE.Rmd’ using rmarkdown
Killed
--- re-building ‘vignette.Rmd’ using rmarkdown
--- finished re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
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:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(remotes)
  > 
  > test_check("remotes")
  
  
  ── 1. Failure: safe_build_package fails appropriately with pkgbuild (@test-insta
  `safe_build_package(...)` threw an error with unexpected message.
  Expected match: "System command error"
  Actual message: "System command 'R' failed, exit status: 1, stdout + stderr:\nE> * checking for file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/remotes.Rcheck/tests/testthat/invalidpkg/DESCRIPTION’ ... OK\nE> * preparing ‘invalidpkg’:\nE> * checking DESCRIPTION meta-information ... ERROR\nE> Malformed Depends or Suggests or Imports or Enhances field.\nE> Offending entries:\nE>   testthat\nE> foobar\nE> Entries must be names of packages optionally followed by '<=' or '>=',\nE> white space, and a valid version number in parentheses.\nE> \nE> See section 'The DESCRIPTION file' in the 'Writing R Extensions'\nE> manual.\nE> "
  Backtrace:
    1. testthat::expect_error(...)
    6. remotes:::safe_build_package(...)
    7. pkgbuild::build(...)
   10. pkgbuild::rcmd_build_tools(...)
   12. callr::rcmd_safe(...)
   13. callr:::run_r(options)
   15. base::with.default(...)
   16. [ base::eval(...) ] with 1 more call
   22. throw(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 396 | SKIPPED: 78 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: safe_build_package fails appropriately with pkgbuild (@test-install.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [17s/52s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("rerddap")
  > 
  > #Sys.setenv(RERDDAP_CACHE_PATH_SUFFIX = "rerddap")
  > cache_setup(temp_dir = TRUE)
  [1] "/tmp/RtmpZEGcIt/R/rerddap"
  > 
  > test_check("rerddap")
  ── 1. Error: convert_units works (@test-convert_units.R#21)  ───────────────────
  Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Backtrace:
   1. testthat::expect_equal(convert_units(udunits = "day"), "d")
   4. rerddap::convert_units(udunits = "day")
   5. cli$get(query = args)
   6. private$make_request(rr)
   7. crul:::crul_fetch(opts)
   8. curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 42 | SKIPPED: 19 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: convert_units works (@test-convert_units.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
Quitting from lines 273-284 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10006 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘UsingrerddapXtracto.Rmd’

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

Error: Vignette re-building failed.
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’,
    ‘R_GlobalContext’

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.
Rd file 'C.FRNN.FRST.Rd':
  \examples lines wider than 100 characters:
                     type.relation = c("tolerance", "eq.1"), t.implicator = "lukasiewicz")                                                   ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rphast.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.
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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ 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/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [32s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: opfw - coverage  (@test_opwf.R#69)  ─────────────────────────────
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests 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) and/or pandoc-citeproc 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
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    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  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
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) and/or pandoc-citeproc 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: ‘rsvg’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Packages suggested but not available for checking: 'ssh', 'aws.s3'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [104s/122s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(antaresViz)
  Loading required package: antaresRead
  Loading required package: antaresProcessing
  
  Attaching package: 'antaresProcessing'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  Loading required package: spMaps
  Loading required package: sp
  Loading required package: raster
  
  Attaching package: 'raster'
  
  The following object is masked from 'package:antaresProcessing':
  
      getValues
  
  Loading required package: rgeos
  rgeos version: 0.5-2, (SVN revision 621)
   GEOS runtime version: 3.6.3-CAPI-1.10.3 
   Linking to sp version: 1.3-2 
   Polygon checking: TRUE 
  
  > 
  > test_check("antaresViz")
  ── 1. Error: (unknown) (@test-h5Request.R#3)  ──────────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
   1. testthat::describe(...)
   2. [ base::eval(...) ] with 1 more call
   6. antaresRead::writeAntaresH5(pathtemp, overwrite = TRUE)
   7. antaresRead::.writeAntaresH5Fun(...)
   8. rhdf5::h5createFile(path)
   9. rhdf5::H5Fcreate(file)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 264 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test-h5Request.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
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  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    testdata   4.2Mb
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.1Mb
    doc    2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.2Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [22s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.9.0 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")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   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)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BFpack.Rcheck/00install.out’ for details.
installed size is 124.9Mb
  sub-directories of 1Mb or more:
    include  124.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.9Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot2f6c215d3771.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2f6c215d3771.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running examples in ‘bigstatsr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.big_SVD
> ### Title: Plot method
> ### Aliases: plot.big_SVD
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)

 *** caught segfault ***
address fae7f000, cause 'invalid permissions'

Traceback:
 1: incr_FBM_mat(X, add)
 2: big_increment(K, tcrossprod(tmp))
 3: big_tcrossprodSelf(X, fun.scaling = fun.scaling, ind.row = ind.row,     ind.col = ind.col, block.size = block.size)
 4: DualBigPCA(X, fun.scaling, ind.row, ind.col, block.size, k)
 5: big_SVD(X, big_scale(), k = 10)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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) and/or pandoc-citeproc 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 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_scan
> ### Title: Example object of class 'scan'
> ### Aliases: example_scan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # get summary of example scan:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> 
> # example_scan was created with:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... is.odimfile -> h5ls -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioRad)
  Welcome to bioRad version 0.4.0
  Warning: no running Docker daemon found Warning: bioRad functionality
  requiring Docker has been disabled
  
  To enable Docker functionality, start Docker and run 'check_docker()'
  in R
  > 
  > test_check("bioRad")
  ── 1. Error: Read a vertical profile (@test-read_vpfiles.R#5)  ─────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_s3_class(readvp(vpfile), "vp")
    4. bioRad::readvp(vpfile)
    5. bioRad::read_vpfiles(...)
    6. bioRad:::read_vp(files)
    7. bioRad::is.vpfile(file)
    8. bioRad::get_odim_object_type(file)
    9. bioRad:::is.odimfile(file)
   10. rhdf5::h5ls(file, recursive = FALSE)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ── 2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13)  ────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_is(readvp.list(c(vpfile, vpfile)), "list")
    4. bioRad::readvp.list(c(vpfile, vpfile))
    5. bioRad::read_vpfiles(...)
    6. base::lapply(files, read_vp)
    7. bioRad:::FUN(X[[i]], ...)
    8. bioRad::is.vpfile(file)
    9. bioRad::get_odim_object_type(file)
   10. bioRad:::is.odimfile(file)
   11. rhdf5::h5ls(file, recursive = FALSE)
   12. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   13. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 2 ]
  1. Error: Read a vertical profile (@test-read_vpfiles.R#5) 
  2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
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’
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))
Error: cons memory exhausted (limit reached?)
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘blockcluster_tutorial.Rnw’ using Sweave
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags

blockcluster version 4.4.3 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>


 *** caught segfault ***
address 10, cause 'memory not mapped'
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.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"),
+    k = 2))
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
> # 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 eff323c, 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 ...
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘BradleyTerryScalable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-128 (BradleyTerryScalable.Rmd) 
Error: processing vignette 'BradleyTerryScalable.Rmd' failed with diagnostics:
The package Matrix.utils is needed for this function to work. Please install it.
--- failed re-building ‘BradleyTerryScalable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

--- re-building ‘break_glm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_glm.Rmd’

--- re-building ‘break_lm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_lm.Rmd’

--- re-building ‘break_randomForest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_randomForest.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘break_ranger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- re-building ‘break_svm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_svm.Rmd’

--- re-building ‘break_xgboost.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_xgboost.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Buddle.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    article   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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 object is masked from 'package:dplyr':

    %>%

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

    grid, legend

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.
Warning in normalizePath(f2) :
  path[1]="webshot60c36aa261cd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot60c36aa261cd.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- 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  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   2.3Mb
Found the following significant warnings:
  circGLM.cpp:256:35: 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:
  circGLM.cpp:895:62: 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:
  circGLM.cpp:896:62: 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/circglmbayes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [33s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 54 | SKIPPED: 0 | WARNINGS: 780 | FAILED: 1 ]
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘RWeka’
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) and/or pandoc-citeproc 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  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.3Mb
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   2.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chamber.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
Timeout was reached: [www.camara.leg.br] Operation timed out after 10148 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘chamber.Rmd’

--- re-building ‘senate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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

--- finished re-building ‘senate.Rmd’

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

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

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   5.9Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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) and/or pandoc-citeproc 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
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    doc   8.0Mb
installed size is  7.7Mb
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    doc    1.5Mb
    libs   5.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'Rmosek', 'gurobi', 'Rcplex', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.3Mb
    help   1.1Mb
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) and/or pandoc-citeproc 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  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (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  5.2Mb
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    img   4.7Mb
installed size is  5.2Mb
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    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is  7.8Mb
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    java   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [27s/136s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(datapackage.r)
  > 
  > test_check("datapackage.r")
  ── 1. Error: remote  ───────────────────────────────────────────────────────────
  Not resolved Remote URI "http://example.com/schema" for descriptor[[schema]]
  Backtrace:
   1. datapackage.r::Package.load(descriptor)
   2. datapackage.r::dereferencePackageDescriptor(descriptor, basePath)
   3. datapackage.r::dereferenceResourceDescriptor(...)
   4. base::tryCatch(...)
   5. base:::tryCatchList(expr, classes, parentenv, handlers)
   6. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7. value[[3L]](cond)
  
  ── 2. Error: remote  ───────────────────────────────────────────────────────────
  Not resolved Remote URI "http://example.com/schema" for descriptor[[schema]]
  Backtrace:
   1. base::eval.parent(Resource.load(descriptor))
   3. datapackage.r::Resource.load(descriptor)
   4. datapackage.r::dereferenceResourceDescriptor(descriptor, basePath)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 247 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: remote 
  2. Error: remote 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.8Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Installation failed.
See ‘/home/ripley/R/packages/tests32/dbarts.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

--- re-building ‘decoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
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 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.0Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Column `item_id` joining character vector and factor, coercing into character vector
Warning: Removed 33 rows containing missing values (geom_point).
Quitting from lines 369-405 (multistage_fundamentals.Rmd) 
Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
Error in solve.default(H * scale, sufI - EsufI) : 
  system is computationally singular: reciprocal condition number = 1.06965e-16

--- failed re-building ‘multistage_fundamentals.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
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 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc           9.8Mb
    htmlwidgets   6.2Mb
Package unavailable to check Rd xrefs: ‘Seurat’
Running examples in ‘diem-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert_to_seurat
> ### Title: Convert an SCE object to Seurat
> ### Aliases: convert_to_seurat
> 
> ### ** Examples
> 
> mm_seur <- convert_to_seurat(x = mb_small, 
+                              targets = FALSE, 
+                              min.features = 500, 
+                              min.cells = 3, 
+                              project = mb_small@name)
Error: Package "Seurat" needed for convert_to_seurat. Please install.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diem.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 305-311 (diem.Rmd) 
Error: processing vignette 'diem.Rmd' failed with diagnostics:
Package "Seurat" needed for convert_to_seurat. Please install.
--- failed re-building ‘diem.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
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
Package suggested but not available for checking: ‘RcppRedis’
Installation failed.
See ‘/home/ripley/R/packages/tests32/DistributionOptimization.Rcheck/00install.out’ for details.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘dmdScheme-Ex.R’ failed
The error most likely occurred in:

> ### Name: report
> ### Title: Generic function for creating a report from an object 'x'
> ### Aliases: report report.character report.dmdScheme_validation
> 
> ### ** Examples
> 
> ## Report of `dmdScheme_validation`
> report( scheme_path_xlsx() )
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’ [29s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > ##
  > library(dmdScheme)
  
  #############################################
  The cache will be in a temporary location and be deleted when you quit R.
  It is located at
     /tmp/RtmpHoai1n/working_dir/Rtmpo4aGrf/dmdScheme_a8c42532dec
  To make it permanent, call
     cache(createPermanent = TRUE)
  and restart R
  and a permanent cache will be created which will survive restarts.
  #############################################
  
  
  trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/dmdScheme_0.9.5.tar.gz'
  Content type 'application/octet-stream' length 27511 bytes (26 KB)
  ==================================================
  downloaded 26 KB
  
  Scheme definition `/tmp/RtmpHoai1n/working_dir/Rtmpo4aGrf/filea8c1e434ec1/dmdScheme_0.9.5.tar.gz, installed with
  name:    dmdScheme
  version: 0.9.5
  Theme switched to dmdScheme_0.9.5
  > ##
  > test_check("dmdScheme")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Start tag expected, '<' not found [4]
Running ‘runit.R’ [17s/29s]
  Running ‘testthat.R’ [19s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h6", "h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Package suggested but not available for checking: ‘doRedis’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
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) and/or pandoc-citeproc 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
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.
Warning in normalizePath(f2) :
  path[1]="webshot66d552745726.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot66d552745726.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- 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  5.0Mb
  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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (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  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
Package suggested but not available for checking: ‘uwot’
Package unavailable to check Rd xrefs: ‘uwot’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.8Mb
Running ‘testthat.R’ [65s/56s]
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
  
  ── 1. Error: write_h5 and read_h5 works (@test-h5.R#11)  ───────────────────────
  HDF5-API 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)
   2. dynutils::read_h5_(file_h5)
   3. hdf5r::h5attr(file_h5, "object_class")
   4. attr_obj$read()
   5. hdf5r:::H5ToR_Pre(mem_type, nelem)
  
  ❌ Unable to read hdf5 files
  ── 2. Error: test_h5_installation works (@test-h5.R#17)  ───────────────────────
  HDF5-API 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())
   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)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 402 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: write_h5 and read_h5 works (@test-h5.R#11) 
  2. Error: test_h5_installation works (@test-h5.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
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) and/or pandoc-citeproc 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"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# 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 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
Package required but not available: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    xsd   4.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
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
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [58s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1326 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 196-208 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
could not find function "rmaxstab"
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests32/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
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   4.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘selectIndicatorsRedRed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Package suggested but not available for checking: ‘multipanelfigure’
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  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
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘formattable-data-frame.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chart_themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Running ‘testthat.R’ [7s/556s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gbfs)
  > 
  > test_check("gbfs")
  ── 1. Error: (unknown) (@test-wrapper.R#7)  ────────────────────────────────────
  Timeout was reached: [biketownpdx.socialbicycles.com] Resolving timed out after 10000 milliseconds
  Backtrace:
    1. gbfs::get_gbfs("portland")
    4. purrr::map2(...)
    5. gbfs:::.f(.x[[i]], .y[[i]], ...)
    9. jsonlite::fromJSON(txt = url)
   10. jsonlite:::parse_and_simplify(...)
   11. jsonlite:::parseJSON(txt, bigint_as_char)
   12. jsonlite:::parse_con(txt, bigint_as_char)
   14. base::open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-wrapper.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.9Mb
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    L8NY18   2.1Mb
    doc      1.0Mb
    libs     2.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    help  26.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/geodiv.Rcheck/00install.out’ for details.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R         9.1Mb
    extdata   1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
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/
Loading required package: raster

Attaching package: 'raster'

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

    maxValue

Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
--- failed re-building ‘geosample-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘geosample-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.4Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.6Mb
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) and/or pandoc-citeproc 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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc         3.0Mb
    tutorials   1.0Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
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.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot215d26338b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot215d26338b.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- 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  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ggplot2-specs.Rmd’

Profiling Timer Expired
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  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) and/or pandoc-citeproc 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 ‘ggseas.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘ggseas.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc         1.3Mb
    libs        1.8Mb
    test_data   1.3Mb
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet plot.cv.relaxed
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> set.seed(1010)
> n = 1000
> p = 100
> nzc = trunc(p/10)
> x = matrix(rnorm(n * p), n, p)
> beta = rnorm(nzc)
> fx = (x[, seq(nzc)] %*% beta)
> eps = rnorm(n) * 5
> y = drop(fx + eps)
> px = exp(fx)
> px = px/(1 + px)
> ly = rbinom(n = length(px), prob = px, size = 1)
> cvob1 = cv.glmnet(x, y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Packages required but not available: 'SeqArray', 'SeqVarTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.3Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 239-240 (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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is 130.8Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    java  128.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    HaDeX   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
prepare_Rd: it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(ce, width.cutoff = 0.75 * getOption("width")) :
  it is not known that wchar_t is Unicode on this platform
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) and/or pandoc-citeproc 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
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘HDclust.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|

 *** caught segfault ***
address 0, cause 'memory not mapped'
Error in !is.character(text) : 
  operations are possible only for numeric, logical or complex types
An irrecoverable exception occurred. R is aborting now ...

 *** caught segfault ***
address 0, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.4Mb
    CWrappers_1.10.3   2.4Mb
    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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

(process:10428): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:10428): Pango-WARNING **: font_face status is: no error has occurred

(process:10428): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:10428): 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
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.3Mb
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) and/or pandoc-citeproc 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 1.0.0

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>
======================

Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.8Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
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 unavailable to check Rd xrefs: ‘RProtoBuf’
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) and/or pandoc-citeproc 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  9.3Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   8.1Mb
    doc    2.7Mb
Running ‘testthat.R’ [4s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  ── 1. Failure: if request_perform() throws an error, RETRY passes it on (@test-r
  `RETRY(...)` threw an error with unexpected message.
  Expected match: "resolve host"
  Actual message: "Could not resolve: 98d90a2a254647889e2e4c236fb576cd.com (Domain name not found)"
  Backtrace:
   1. testthat::expect_error(...)
   6. httr::RETRY(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: if request_perform() throws an error, RETRY passes it on (@test-retry.R#18) 
  
  Error: testthat unit tests 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (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
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) and/or pandoc-citeproc 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
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
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) and/or pandoc-citeproc 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
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
Package unavailable to check Rd xrefs: ‘BSgenome.Mmusculus.UCSC.mm10’
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-70 (example.Rmd) 
Quitting from lines 62-70 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
    doc    1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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 ...
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
> 
> ### ** Examples
> 
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error: C stack usage  229807252 is too close to the limit
Error: The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1347-1404 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       5.4Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      4.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.8Mb
Package unavailable to check Rd xrefs: ‘minfi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#80)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-operators.R#68)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 806 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: in-place operators work in common cases (@test-operators.R#80) 
  2. Failure: in-place operators work in common cases (@test-operators.R#68) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. io:::test_read_write_read(f)
    2. io::qread(infile) /home/ripley/R/packages/tests32/io.Rcheck/tests/helper.R:47:8
    4. io:::qread.hdf5(...)
   10. rhdf5::h5ls(file)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.7Mb
Package suggested but not available for checking: ‘redux’
Running examples in ‘iRefR-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert_MITAB_to_edgeList
> ### Title: Convert MITAB format to edgeList format
> ### Aliases: convert_MITAB_to_edgeList
> 
> ### ** Examples
> 
>      ## get tables
>      irefindex_curr_ecoli = get_irefindex("562", "13.0", tempdir())
Downloading iRefIndex file...
trying URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Warning in download.file(url, destfile = zipfile) :
  URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip': status was 'Couldn't connect to server'
Error in download.file(url, destfile = zipfile) : 
  cannot open URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Calls: get_irefindex -> download.file
Execution halted
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) and/or pandoc-citeproc 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
Running ‘testthat.R’ [4s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(itunesr)
  > 
  > test_check("itunesr")
  ── 1. Error: The output dataframe Type is  (@test-fun.R#7)  ────────────────────
  attempt to set an attribute on NULL
  Backtrace:
   1. testthat::expect_equal(...)
   4. itunesr::getReviews("297606951", "in", 2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: The output dataframe Type is  (@test-fun.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘joinet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.joinet
> ### Title: Extract Coefficients
> ### Aliases: coef.joinet
> 
> ### ** Examples
> 
> n <- 50; p <- 100; q <- 3
> X <- matrix(rnorm(n*p),nrow=n,ncol=p)
> Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
> object <- joinet(Y=Y,X=X)
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: joinet ... NextMethod -> predict.glmnet -> lambda.interp -> approx
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(joinet)
  > 
  > testthat::test_check(package="joinet",stop_on_warning=FALSE)
  ── 1. Error: (unknown) (@test.R#24)  ───────────────────────────────────────────
  need at least two non-NA values to interpolate
  Backtrace:
    1. joinet::joinet(...)
    2. glmnet::cv.glmnet(...)
    3. glmnet:::cv.glmnet.raw(...)
    5. glmnet:::buildPredmat.default(...)
    9. glmnet::predict.glmnet(...)
   10. glmnet:::lambda.interp(lambda, s)
   11. stats::approx(lambda, seq(lambda), sfrac)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘article.Rmd’

--- re-building ‘joinet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 105-106 (joinet.Rmd) 
Error: processing vignette 'joinet.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘joinet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Package suggested but not available for checking: ‘gifski’
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 3.0-2

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

--- re-building ‘fixed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘fixed.Rmd’

--- re-building ‘hiv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘hiv.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘knockoff.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loaded glmnet 3.0-2

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12751 - 6375 == 6375
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘copper_mining_2d.Rmd’

--- re-building ‘ordinary_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ordinary_kriging.Rmd’

--- re-building ‘simple_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘simple_kriging.Rmd’

--- re-building ‘universal_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘universal_kriging.Rmd’

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.3Mb
    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  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    libs   2.3Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
Compilation used the following non-portable flag(s):
  ‘-mt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch_import.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘batch_import.Rmd’

--- re-building ‘renormalise.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘renormalise.Rmd’

--- re-building ‘true_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 59-62 (true_example.Rmd) 
Error: processing vignette 'true_example.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘true_example.Rmd’

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

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

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)
> 
> # Test different settings
> plot_superpixels(image, n_superpixels = 100, colour = 'white')

 *** caught segfault ***
address 2c, cause 'memory not mapped'

Traceback:
 1: magick_image_convolve_kernel(image, kernel, iterations, scaling,     bias)
 2: magick::image_convolve(contour, "Laplacian")
 3: plot_superpixels(image, n_superpixels = 100, colour = "white")
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Understanding_lime.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/lmSubsets.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LUCIDus-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help   1.3Mb
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	| 
Step  5	| 
Step  6	| 
Step  7	| 
Step  8	| 
Step  9	| 
Step  10	| 
Step  11	|
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 0.6-5
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> 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  333747348 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  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> ### Name: analysis
> ### Title: Image Analysis
> ### Aliases: analysis image_compare image_compare_dist image_fft
> 
> ### ** Examples
> 
> out1 <- image_blur(logo, 3)

 *** caught segfault ***
address 2c, cause 'memory not mapped'

Traceback:
 1: magick_image_blur(image, radius, sigma)
 2: image_blur(logo, 3)
An irrecoverable exception occurred. R is aborting now ...
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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

Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘manhattanly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot3345668d163.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3345668d163.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- 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  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (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  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MBNMAtime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Reference treatment is `plac`

ET50 parameters (beta.2) are on exponential scale to ensure they take positive values on the natural scale
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
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
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs   1.7Mb
    misc   1.1Mb
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) and/or pandoc-citeproc 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnosticPlotting.Rmd’ using knitr
Loading required package: miceRanger
--- finished re-building ‘diagnosticPlotting.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘miceAlgorithm.Rmd’ using knitr
--- re-building ‘usingMiceRanger.Rmd’ using knitr
Loading required package: miceRanger
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
--- finished re-building ‘usingMiceRanger.Rmd’

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

Error: Vignette re-building failed.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:4350): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:4350): Pango-WARNING **: font_face status is: <unknown error status>

(process:4350): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:4350): 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) and/or pandoc-citeproc 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 unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 172-173 (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
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking: 'FSelector', 'RWeka'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
    help   1.4Mb
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: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
Running ‘testthat.R’ [9s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("MODISTools")
  Loading required package: MODISTools
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  ── 1. Error: test mt_batch_subset() (@test_download_functions.R#218)  ──────────
  2 nodes produced errors; first error: Your requested timed out or the server is unreachable
  Backtrace:
   1. testthat::expect_is(...)
   4. MODISTools::mt_batch_subset(...)
   5. parallel::parRapply(...)
   7. parallel::clusterApply(...)
   8. parallel:::staticClusterApply(cl, fun, length(x), argfun)
   9. parallel:::checkForRemoteErrors(val)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: test mt_batch_subset() (@test_download_functions.R#218) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In for (name in names(public_methods)) lockBinding(name, public_bind_env) :
    closing unused connection 5 (<-localhost:11257)
  2: In for (name in names(public_methods)) lockBinding(name, public_bind_env) :
    closing unused connection 4 (<-localhost:11257)
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
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  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (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
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot694b4e567412.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot694b4e567412.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  Error: Reason: On Solaris
  Execution halted
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 2.5-1 (2019-12-12) 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: maps
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.
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

 *** caught segfault ***
address ed35c896, cause 'memory not mapped'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 73-74 (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  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    CppCode  10.4Mb
    R         6.2Mb
    include   5.3Mb
    libs      2.8Mb
    tests     1.7Mb
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) and/or pandoc-citeproc 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 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Found the following significant warnings:
  WrapperNMFGPU.cpp:96:12: warning: converting ‘false’ to pointer type for argument 1 of ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/nmfgpu4R.Rcheck/00install.out’ for details.
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: 0.029 0.028 0.058
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   8.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd) 
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘NormalizeMets_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.8Mb
    help   2.6Mb
Packages suggested but not available for checking: 'RMark', 'R2ucare'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     4.1Mb
    models   4.4Mb
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
> #Constrain unique variances equal:
> factorModel2 <- omxSetParameters(
+ 	model=factorModel1,labels=paste("u",1:5,sep=""),
+ 	newlabels="u",name="OneFactor2")
> factorFit2 <- mxRun(factorModel2)
Running OneFactor2 with 6 parameters
Error: C stack usage  204182676 is too close to the limit
Error: The job for model 'OneFactor2' 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
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
Running ‘testthat.R’ [14s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  ── 1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.
  coef(o) not equal to `coefg`.
  3/7 mismatches (average diff: 0.475)
  [1] -0.572 - 0 == -0.572
  [3] -0.440 - 0 == -0.440
  [4] -0.413 - 0 == -0.413
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#213) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.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  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests32/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  Backtrace:
   1. testthat::expect_error(quickSetupOxcal(), NA)
   6. oxcAAR::quickSetupOxcal()
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests 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) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-30 (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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (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:
    data        1.6Mb
    localdata   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘functionMaximization.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Running initial scoring function 3 times in 1 thread(s)...  0.549 seconds

Starting Epoch 1
  1) Fitting Gaussian Process...
  2) Running local optimum search...        2.345 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.198 seconds

Starting Epoch 2
  1) Fitting Gaussian Process...
  2) Running local optimum search...        1.084 seconds
  3) Running FUN 1 times in 1 thread(s)...  0.199 seconds
Warning in sink() : no sink to remove
Warning in sink() : no sink to remove
--- finished re-building ‘functionMaximization.Rmd’

--- re-building ‘multiPointSampling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘multiPointSampling.Rmd’

--- re-building ‘tuningHyperparameters.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Running initial scoring function 4 times in 1 thread(s)...Error: segfault from C stack overflow
Warning in sink() : no sink to remove
Execution halted
SUMMARY: processing the following file failed:
  ‘tuningHyperparameters.Rmd’

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(parglm)
  > 
  > test_check("parglm")
  
   *** caught segfault ***
  address ce257536, cause 'memory not mapped'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        2.3Mb
    testdata   1.8Mb
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  6.3Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   8.4Mb
Package unavailable to check Rd xrefs: ‘tesseract’
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.pense
> ### Title: Extract Model Coefficients
> ### Aliases: coef.pense
> 
> ### ** Examples
> 
> # Generate data with highly correlated groups of variables and some outliers
> set.seed(12345)
> n <- 50
> n_out <- 3
> p <- 20
> x <- 1 + matrix(rnorm(n * p), ncol = p)
> x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
> x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
> 
> y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
> 
> y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
> 
> # Compute the PENSE estimator
> set.seed(1234)
> est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: enpy_exact(x, y, alpha, lambda, options, en_options)
 2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 4: FUN(X[[i]], ...)
 5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-62 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data       2.4Mb
    examples   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.5Mb
installed size is  6.0Mb
  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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Running ‘testthat.R’ [109s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PlackettLuce)
  > 
  > test_check("PlackettLuce")
  ── 1. Error: (unknown) (@test-log-likelihood.R#81)  ────────────────────────────
  The package Matrix.utils is needed for this function to work. Please install it.
  Backtrace:
   1. BradleyTerryScalable::btdata(as.data.frame(cbind(M, 1)))
   2. BradleyTerryScalable:::pairs_to_matrix(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 168 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-log-likelihood.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 138-146 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘using_plotdap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.4Mb
Running ‘testthat.R’ [156s/198s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  ── 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ─────────
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1370 | SKIPPED: 45 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [55s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmml, quietly = T)
  > 
  > test_check("pmml")
  Error: segfault from C stack overflow
  Execution halted
Running ‘testthat.R’ [48s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ── 1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertp
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 6 - 0 == 6
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1561 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertpmultinom.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R      7.0Mb
    data   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: 'heatmap' objects don't have these attributes: 'showlegend'
Valid attributes include:
'type', 'visible', 'opacity', 'name', 'uid', 'ids', 'customdata', 'meta', 'hoverinfo', 'hoverlabel', 'stream', 'transforms', 'uirevision', 'z', 'x', 'x0', 'dx', 'y', 'y0', 'dy', 'text', 'hovertext', 'transpose', 'xtype', 'ytype', 'zsmooth', 'connectgaps', 'xgap', 'ygap', 'zhoverformat', 'hovertemplate', 'zauto', 'zmin', 'zmax', 'zmid', 'colorscale', 'autocolorscale', 'reversescale', 'showscale', 'colorbar', 'coloraxis', 'xcalendar', 'ycalendar', 'xaxis', 'yaxis', 'idssrc', 'customdatasrc', 'metasrc', 'hoverinfosrc', 'zsrc', 'xsrc', 'ysrc', 'textsrc', 'hovertextsrc', 'hovertemplatesrc', 'key', 'set', 'frame', 'transforms', '_isNestedKey', '_isSimpleKey', '_isGraticule', '_bbox'

Warning in normalizePath(f2) :
  path[1]="webshot18452bee2e5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot18452bee2e5.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/PPRL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rmosek’
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'lpsymphony', 'Rsymphony'
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc           9.3Mb
    htmlwidgets   2.7Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Backtrace:
    █
 1. └─profile::write_pprof(ds, pprof_file)
 2.   └─profile:::ds_to_msg(x)
 3.     └─profile:::provide_proto()
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/promotionImpact.Rcheck/00install.out’ for details.
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:
    dict   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.3Mb
    examples   2.9Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (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
Running examples in ‘pyinit-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyinit
> ### Title: PY (Pena-Yohai) initial estimates for S-estimates of regression
> ### Aliases: pyinit
> 
> ### ** Examples
> 
> # generate a simple synthetic data set for a linear regression model
> # with true regression coefficients all equal to one "(1, 1, 1, 1, 1)"
> set.seed(123)
> x <- matrix(rnorm(100*4), 100, 4)
> y <- rnorm(100) + rowSums(x) + 1
> # add masked outliers
> a <- svd(var(x))$v[,4]
> x <- rbind(x, t(outer(a, rnorm(20, mean=4, sd=1))))
> y <- c(y, rnorm(20, mean=-2, sd=.2))
> 
> # these outliers are difficult to find
> plot(lm(y~x), ask=FALSE)
> 
> # use pyinit to obtain estimated regression coefficients
> tmp <- pyinit(x=x, y=y, resid_keep_method='proportion', psc_keep = .5, resid_keep_prop=.5)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    gui          1.3Mb
    staticdocs   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/qgg.Rcheck/00install.out’ for details.
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 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) and/or pandoc-citeproc 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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quadmesh.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-35 (quadmesh.Rmd) 
Error: processing vignette 'quadmesh.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quadmesh.Rmd’

--- re-building ‘topography.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 19-33 (topography.Rmd) 
Error: processing vignette 'topography.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘topography.Rmd’

SUMMARY: processing the following files failed:
  ‘quadmesh.Rmd’ ‘topography.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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.4Mb
    libs   1.2Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Running ‘RUnit.R’ [149s/192s]
Running the tests in ‘tests/RUnit.R’ failed.
Complete output:
  > if (requireNamespace("RUnit", quietly=TRUE) && requireNamespace("RcppXPtrUtils", quietly=TRUE) && requireNamespace("r2sundials", quietly=TRUE) && requireNamespace("RcppArmadillo", quietly=TRUE)) {
  +    library(RUnit)
  +    library(RcppXPtrUtils)
  +    library(r2sundials)
  +    library(RcppArmadillo)
  + 
  +    testSuite <- defineTestSuite(
  +       name = "r2sundials unit tests",
  +       dirs = system.file("unitTests", package = "r2sundials"),
  +       testFuncRegexp = "^[Tt]est.+"
  +    )
  +    Sys.setenv("R_TESTS"="")
  +    tests <- runTestSuite(testSuite)
  + 
  +    printTextProtocol(tests)
  + 
  +    if (getErrors(tests)$nFail > 0) stop("RUnit test failure")
  +    if (getErrors(tests)$nErr > 0) stop("Errors in RUnit tests")
  + }
  Loading required package: rmumps
  
  Attaching package: 'r2sundials'
  
  The following object is masked from 'package:rmumps':
  
      get_cnst
  
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  CC: Warning: Optimizer level changed from 0 to 3 to support parallelized code.
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  CVode: At t = 6.69434e+10, mxstep steps taken before reaching tout.
Package unavailable to check Rd xrefs: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
RAbHIT version: 0.1.4
Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
Quitting from lines 299-301 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘RAbHIT-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    app   6.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
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) and/or pandoc-citeproc 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’ [182s/224s]
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/RtmpQEa4.E/working_dir/Rtmpq0aqXQ/file558a46bb69ed/2_6': no such file or directory
  ── 1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#
  [ENOENT] Failed to stat '/tmp/RtmpQEa4.E/working_dir/Rtmpq0aqXQ/file558a46bb69ed/2_6': no such file or directory
  
  Backtrace:
   1. randomsearch::randomsearch(...)
   2. randomsearch:::randomsearch.smoof_function(...)
   3. parallelMap::parallelMap(...)
   4. parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5. parallelMap:::stopWithJobErrorMessages(...)
   6. BBmisc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

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 object is masked from 'package:base':

    date

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 130-141 (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  9.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.5Mb
    etc    2.2Mb
    po     1.5Mb
Package suggested but not available for checking: ‘av’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.7Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.4Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons.
> ### Aliases: icon
> 
> ### ** Examples
> 
> rmd <- '
+ ```{r}
+ library(rchallenge)
+ ```
+ <link rel="stylesheet" 
+  href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
+ `r icon("fa-user")`
+ `r icon("fa-user fa-lg")`
+ `r icon("fa-user fa-2x")`
+ `r icon("fa-user fa-3x")`
+ `r icon("fa-user fa-3x fa-border")`
+ '
> file <- tempfile()
> cat(rmd, file=file)
> writeLines(readLines(file))

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppAnnoy.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
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) and/or pandoc-citeproc 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>

--- 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) and/or pandoc-citeproc 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'
--- 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
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 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   6.6Mb
Running ‘testthat.R’ [18s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ── 1. Failure: csf algorithm works (@test-CSF.R#7)  ────────────────────────────
  length(id_ground) %in% c(15459L, 15453L) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: csf algorithm works (@test-CSF.R#7) 
  
  Error: testthat unit tests 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) and/or pandoc-citeproc 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning: filter_() is deprecated. 
Please use filter() instead

The 'programming' vignette or the tidyeval book can help you
to program with filter() : https://tidyeval.tidyverse.org
This warning is displayed once per session.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Running ‘testthat.R’ [11s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(remotes)
  > 
  > test_check("remotes")
  
  
  ── 1. Failure: safe_build_package fails appropriately with pkgbuild (@test-insta
  `safe_build_package(...)` threw an error with unexpected message.
  Expected match: "System command error"
  Actual message: "System command 'R' failed, exit status: 1, stdout + stderr:\nE> * checking for file ‘/home/ripley/R/packages/tests32/remotes.Rcheck/tests/testthat/invalidpkg/DESCRIPTION’ ... OK\nE> * preparing ‘invalidpkg’:\nE> * checking DESCRIPTION meta-information ... ERROR\nE> Malformed Depends or Suggests or Imports or Enhances field.\nE> Offending entries:\nE>   testthat\nE> foobar\nE> Entries must be names of packages optionally followed by '<=' or '>=',\nE> white space, and a valid version number in parentheses.\nE> \nE> See section 'The DESCRIPTION file' in the 'Writing R Extensions'\nE> manual.\nE> "
  Backtrace:
    1. testthat::expect_error(...)
    6. remotes:::safe_build_package(...)
    7. pkgbuild::build(...)
   10. pkgbuild::rcmd_build_tools(...)
   12. callr::rcmd_safe(...)
   13. callr:::run_r(options)
   15. base::with.default(...)
   16. [ base::eval(...) ] with 1 more call
   22. throw(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 393 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: safe_build_package fails appropriately with pkgbuild (@test-install.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'rENA'

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

    show

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 107-117 (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 ‘means-rotation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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


Attaching package: 'rENA'

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

    show

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [29s/47s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("rerddap")
  > 
  > #Sys.setenv(RERDDAP_CACHE_PATH_SUFFIX = "rerddap")
  > cache_setup(temp_dir = TRUE)
  [1] "/tmp/RtmpoeaOBm/working_dir/RtmpmcaGPx/R/rerddap"
  > 
  > test_check("rerddap")
  ── 1. Error: convert_units works (@test-convert_units.R#15)  ───────────────────
  Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Backtrace:
   1. testthat::expect_equal(convert_units(udunits = "degC"), "Cel")
   4. rerddap::convert_units(udunits = "degC")
   5. cli$get(query = args)
   6. private$make_request(rr)
   7. crul:::crul_fetch(opts)
   8. curl::curl_fetch_memory(x$url$url, handle = x$url$handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 36 | SKIPPED: 19 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: convert_units works (@test-convert_units.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 155-159 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10010 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘UsingrerddapXtracto.Rmd’

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

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

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
prtconf: devinfo facility not available
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
prtconf: devinfo facility not available
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
prtconf: devinfo facility not available
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
prtconf: devinfo facility not available
prtconf: devinfo facility not available
prtconf: devinfo facility not available
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
prtconf: devinfo facility not available
prtconf: devinfo facility not available
prtconf: devinfo facility not available
prtconf: devinfo facility not available
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘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
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) and/or pandoc-citeproc 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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- 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) and/or pandoc-citeproc 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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- 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  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    doc       1.4Mb
    extdata   2.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
NOTE: The default cutoff when expanding a 2-digit year
to a 4-digit year will change from 30 to 69 by Aug 2020
(as for Date and POSIXct in base R.)
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 object is masked from 'package:base':

    date

Quitting from lines 50-63 (precipitation_stochastic_generation_v6.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v6.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘precipitation_stochastic_generation_v6.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v6.Rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.6Mb
    libs    1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'playwith', 'pmg', 'rggobi', 'SVGAnnotation'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
Package required but not available: ‘RPostgres’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  atkClasses.c:1054:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1062:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1401:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1974:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1990:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8831:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11314:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/RGtk2.Rcheck/00install.out’ for details.
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.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.3Mb
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) and/or pandoc-citeproc 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
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)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
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) and/or pandoc-citeproc 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 2.5-1 (2019-12-12) 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: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Quitting from lines 66-67 (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 ‘RobStatTM-Ex.R’ failed
The error most likely occurred in:

> ### Name: lmrobdet.control
> ### Title: Tuning parameters for lmrobdetMM and lmrobdetDCML
> ### Aliases: lmrobdet.control
> 
> ### ** Examples
> 
> data(coleman, package='robustbase')
> m2 <- lmrobdetMM(Y ~ ., data=coleman, control=lmrobdet.control(refine.PY=50))

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: pyinit::pyinit(x = X, y = y, intercept = FALSE, delta = dee,     cc = 1.54764, psc_keep = control$psc_keep * (1 - (p/n)),     resid_keep_method = control$resid_keep_method, resid_keep_thresh = control$resid_keep_thresh,     resid_keep_prop = control$resid_keep_prop, maxit = control$py_maxit,     eps = control$py_eps, mscale_maxit = control$mscale_maxit,     mscale_tol = control$mscale_tol, mscale_rho_fun = "bisquare")
 2: MMPY(X = x, y = y, control = control, mf = mf)
 3: lmrobdetMM(Y ~ ., data = coleman, control = lmrobdet.control(refine.PY = 50))
An irrecoverable exception occurred. R is aborting now ...
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 10, 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 ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/RODBCext.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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
Installation failed.
See ‘/home/ripley/R/packages/tests32/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
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) and/or pandoc-citeproc 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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using Sweave
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, which.max, which.min


Attaching package: ‘rsolr’

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

    ftable

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

    grouping


Error: processing vignette 'intro.Rnw' failed with diagnostics:
 chunk 3 (label = SolrFrame) 
Error in value[[3L]](cond) : Failed to retrieve schema.
rsolr requires schema via REST or as XML from admin module.
Error from REST: Error: Internal Server Error



--- failed re-building ‘intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [30m/34m]
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")
Package required but not available: ‘GMMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    4.9Mb
    libs  10.9Mb
installed size is 11.5Mb
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    libs        8.5Mb
    unitTests   1.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running examples in ‘RSuite-Ex.R’ failed
The error most likely occurred in:

> ### Name: prj_pack
> ### Title: Prepares project source pack tagged with version.
> ### Aliases: prj_pack
> 
> ### ** Examples
> 
> # create exemplary project base folder
> prj_base <- tempfile("example_")
> dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)
> 
> # start project
> prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)
2020-02-09 22:39:00 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.37.253).
2020-02-09 22:39:00 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2020-02-09 22:39:00 INFO:rsuite:Package mypackage started in project my_project.
> 
> # build project source pack
> pack_fpath <- prj_pack(prj = prj, path = tempdir(), pack_ver = "1.0")
2020-02-09 22:39:00 WARNING:rsuite:Project environment is not locked!
2020-02-09 22:39:00 INFO:rsuite:Exporting project from /tmp/Rtmpi9ayBW/working_dir/RtmpzsaGkf/example_a54eaf397/my_project ...
2020-02-09 22:39:00 INFO:rsuite:Exporting project from /tmp/Rtmpi9ayBW/working_dir/RtmpzsaGkf/example_a54eaf397/my_project ... done
2020-02-09 22:39:02 WARNING:rsuite:Zip building aborted for /tmp/Rtmpi9ayBW/working_dir/RtmpzsaGkf/prjpack_my_project_1.0x.zip
2020-02-09 22:39:02 ERROR:rsuite:Failed to create pack file (zip returned non 0 return status).
Error: Failed to create pack file (zip returned non 0 return status).
Execution halted
installed size is  6.2Mb
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installed size is 11.1Mb
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installed size is  5.8Mb
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installed size is  5.2Mb
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installed size is  7.5Mb
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    libs      3.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc           3.3Mb
    htmlwidgets   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘R-versus-CPP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘R-versus-CPP.Rmd’

SUMMARY: processing the following file failed:
  ‘R-versus-CPP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
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    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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 63.6Mb
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    extdata  63.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘sass.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'pogs'
installed size is  5.0Mb
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    example   2.7Mb
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installed size is  5.3Mb
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    vignette_data   2.1Mb
installed size is  8.2Mb
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installed size is  5.0Mb
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    extdata   4.1Mb
installed size is  7.9Mb
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installed size is  8.5Mb
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    doc    6.3Mb
    libs   1.0Mb
installed size is  6.1Mb
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    sequences   2.1Mb
installed size is  5.5Mb
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    vcf    1.0Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
> 
> ### ** Examples
> 
> if (.Platform$endian == "little") {
+   param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+                 geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
+   param <- makeAnnotationParameter(param)
+   print(param)
+   annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
+ } else {
+   message("Tabix does not work well for big endian for now")
+ }
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"

$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"

$geneFileFormat
[1] "refFlat"

$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"

$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
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    extdata   1.3Mb
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> ### Name: LR.intersect
> ### Title: Function for identifying contradictory simplifying assumptions
> ###   or easy counterfactuals.
> ### Aliases: LR.intersect
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)

 *** caught segfault ***
address fa88af00, cause 'memory not mapped'

Traceback:
 1: minimize(SCHF, outcome = "EXPORT", conditions = c("EMP", "BARGAIN",     "UNI", "OCCUP", "STOCK", "MA"), incl.cut = 0.9, include = "?",     details = TRUE, show.cases = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: 'RcppAnnoy', 'uwot'

Packages suggested but not available for checking: 'loomR', 'monocle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.8Mb
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    doc     12.4Mb
    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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
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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) and/or pandoc-citeproc 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
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    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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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) and/or pandoc-citeproc 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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    framework7-5.1.3   1.7Mb
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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) and/or pandoc-citeproc 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigminer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
stdin: not in compressed format
Quitting from lines 59-61 (sigminer.Rmd) 
Error: processing vignette 'sigminer.Rmd' failed with diagnostics:
missing required fields from MAF: Hugo_Symbol
--- failed re-building ‘sigminer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
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installed size is  5.1Mb
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    doc    2.7Mb
installed size is  5.0Mb
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installed size is  5.9Mb
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Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basics.Rmd’

--- re-building ‘iframes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-87 (iframes.Rmd) 
Error: processing vignette 'iframes.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘iframes.Rmd’

--- re-building ‘pdfs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-33 (pdfs.Rmd) 
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘pdfs.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 88-93 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘plots.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘iframes.Rmd’ ‘pdfs.Rmd’ ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CustomTable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘CustomTable.Rmd’

--- re-building ‘SmartEDA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 132-133 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
--- failed re-building ‘SmartEDA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
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    R     1.0Mb
    doc   2.9Mb
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installed size is  5.1Mb
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    data   1.6Mb
    doc    1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘shiny_apps.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny_apps.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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.
Warning in normalizePath(f2) :
  path[1]="webshot6a294e4f3cbb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot6a294e4f3cbb.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘understanding_sortable_js.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
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    doc   4.1Mb
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) and/or pandoc-citeproc 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, which.max, which.min

Identifing all possible orderings..
Total run time: 2.73 secs
Identifing all possible orderings..
Total run time: 1.44 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 ‘lint.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  ── 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  error in running command: 'Illegal seek'
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy(ask = FALSE)
   3. spacyr:::check_spacy_model(py_exec, model)
   6. base::system2(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 51 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
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) and/or pandoc-citeproc 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  5.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    java   3.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      5.5Mb
    doc    5.1Mb
    help   5.3Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    lib       1.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc  10.6Mb
    nc    4.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘stRvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [0m/85m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subgroup.discovery)
  > 
  > test_check("subgroup.discovery")
  
   *** caught segfault ***
  address 17c, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.5Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: segfault from C stack overflow
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    help   1.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.3Mb
    doc    3.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.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:
    extdata   4.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HTML.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
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

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
Loading required package: Hmisc
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

--- finished re-building ‘tables.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           1.9Mb
    simulations   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.9Mb
Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi'
Running ‘testthat.R’ [27s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(texPreview)
  > test_check("texPreview")
  ── 1. Error: (unknown) (@test-tex.R#115)  ──────────────────────────────────────
  R: delegate failed `'potrace' --svg --output '%o' '%i'' @ error/delegate.c/InvokeDelegate/1958
  Backtrace:
    1. testthat::describe(...)
    2. [ base::eval(...) ] with 1 more call
    5. texPreview:::tex_preview.xtable(...)
    7. texPreview:::tex_preview.character(...)
    8. texPreview:::tex_preview.default(...)
    9. texPreview:::tex_image(obj, stem, write_flag, overwrite)
   10. magick::image_write(imgOut, tex_path(fileDir, stem, dev = imgFormat))
   11. magick:::magick_image_write(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-tex.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2

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

sh: nproc:  not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
--- failed re-building ‘Tigger-Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘dbarts’
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) and/or pandoc-citeproc 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  5.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Package suggested but not available for checking: ‘moveVis’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
Package unavailable to check Rd xrefs: ‘moveVis’
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) and/or pandoc-citeproc 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

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  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.1Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 130-139 (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
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
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
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius 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
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TSplotly.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: TSplotly
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Loading required package: plotly

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: forecast
Quitting from lines 99-117 (TSplotly.Rmd) 
Error: processing vignette 'TSplotly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TSplotly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    fonts   2.9Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc     6.9Mb
    ubinc   2.2Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc         7.3Mb
    dummydata   1.5Mb
    libs        1.9Mb
Package suggested but not available for checking: ‘TSstudio’
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (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  5.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   1.9Mb
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
Running ‘spelling.R’
  Running ‘testthat.R’ [34s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usethis)
  > 
  > test_check("usethis")
  ── 1. Failure: use_logo() doesn't error (@test-use-logo.R#9)  ──────────────────
  `use_logo("logo.png")` threw an error.
  Message: R: negative or zero image size `' @ error/image.c/CloneImage/812
  Class:   Magick::ErrorCorruptImage/C++Error/error/condition
  Backtrace:
   1. usethis:::expect_error_free(use_logo("logo.png"))
   7. usethis::use_logo("logo.png")
   8. magick::image_write(img_data, logo_path)
   9. magick:::magick_image_write(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 418 | SKIPPED: 16 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: use_logo() doesn't error (@test-use-logo.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   6.6Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package required but not available: ‘RcppAnnoy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
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:ranger':

    importance

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) and/or pandoc-citeproc 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
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) and/or pandoc-citeproc 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:
cannot open the connection
--- 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  7.3Mb
  sub-directories of 1Mb or more:
    R   2.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    1.3Mb
    help   3.0Mb
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) and/or pandoc-citeproc 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:
cannot open the connection
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-visNetwork.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [24s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vroom)
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("vroom", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("vroom")
  + }
  Loading required namespace: xml2
  ── 1. Error: vroom works with many connections (@test-multi-file.R#90)  ────────
  Evaluation error: cannot open the connection.
  Backtrace:
   1. vroom::vroom(files)
   2. vroom:::vroom_(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 691 | SKIPPED: 5 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: vroom works with many connections (@test-multi-file.R#90) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In for (n in impnames) if (!is.null(genImp <- impenv[[n]])) { :
    closing unused connection 4 (/tmp/RtmpXOaGfx/working_dir/RtmpJYaG7M/file4ddc79a727d/129.csv.gz)
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.6Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bn   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- 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
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) and/or pandoc-citeproc 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 rows 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
Running ‘testthat.R’ [13s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: opfw - coverage  (@test_opwf.R#69)  ─────────────────────────────
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/x12.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/ripley/R/packages/tests32/x13binary.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> ### Name: cb.gblinear.history
> ### Title: Callback closure for collecting the model coefficients history
> ###   of a gblinear booster during its training.
> ### Aliases: cb.gblinear.history
> 
> ### ** Examples
> 
> #### Binary classification:
> #
> # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
> # without considering the 2nd order interactions:
> require(magrittr)
Loading required package: magrittr
> x <- model.matrix(Species ~ .^2, iris)[,-1]
> colnames(x)
 [1] "Sepal.Length"              "Sepal.Width"              
 [3] "Petal.Length"              "Petal.Width"              
 [5] "Sepal.Length:Sepal.Width"  "Sepal.Length:Petal.Length"
 [7] "Sepal.Length:Petal.Width"  "Sepal.Width:Petal.Length" 
 [9] "Sepal.Width:Petal.Width"   "Petal.Length:Petal.Width" 
> dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"))
> param <- list(booster = "gblinear", objective = "reg:logistic", eval_metric = "auc",
+               lambda = 0.0003, alpha = 0.0003, nthread = 2)
> # For 'shotgun', which is a default linear updater, using high eta values may result in
> # unstable behaviour in some datasets. With this simple dataset, however, the high learning
> # rate does not break the convergence, but allows us to illustrate the typical pattern of
> # "stochastic explosion" behaviour of this lock-free algorithm at early boosting iterations.
> bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 1.,
+                  callbacks = list(cb.gblinear.history()))
Error: segfault from C stack overflow
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.047136 
  Error: segfault from C stack overflow
  Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Running ‘testthat.R’ [5s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xml2)
  > 
  > test_check("xml2")
  This is libxml2 version 2.9.9 
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Document is empty [4]
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
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.
Found the following significant warnings:
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘readwriteplot.Rmd’ using rmarkdown
Quitting from lines 22-28 (readwriteplot.Rmd) 
Error: processing vignette 'readwriteplot.Rmd' failed with diagnostics:
SSL: certificate subject name (*.uberspace.de) does not match target host name 'ex.volkerschmid.de'
--- failed re-building ‘readwriteplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/circglmbayes.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DistributionOptimization.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(itunesr)
  > 
  > test_check("itunesr")
  ── 1. Error: The output dataframe Type is  (@test-fun.R#7)  ────────────────────
  attempt to set an attribute on NULL
  Backtrace:
   1. testthat::expect_equal(...)
   4. itunesr::getReviews("297606951", "in", 2)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: The output dataframe Type is  (@test-fun.R#7) 
  
  Error: testthat unit tests failed
  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:182:19: 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:896:16: 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:196:19: 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.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  migrate.c:180:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:187:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:200:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:287:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:313:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:560:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:596:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:604:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘arrow’
Running ‘testthat.R’ [81s/88s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PlackettLuce)
  > 
  > test_check("PlackettLuce")
  ── 1. Error: (unknown) (@test-log-likelihood.R#81)  ────────────────────────────
  The package Matrix.utils is needed for this function to work. Please install it.
  Backtrace:
   1. BradleyTerryScalable::btdata(as.data.frame(cbind(M, 1)))
   2. BradleyTerryScalable:::pairs_to_matrix(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 168 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-log-likelihood.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [150s/150s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  ── 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ─────────
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1390 | SKIPPED: 43 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
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:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(remotes)
  > 
  > test_check("remotes")
  
  
  ── 1. Failure: safe_build_package fails appropriately with pkgbuild (@test-insta
  `safe_build_package(...)` threw an error with unexpected message.
  Expected match: "System command error"
  Actual message: "System command 'R' failed, exit status: 1, stdout + stderr:\nE> * checking for file ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/remotes.Rcheck/tests/testthat/invalidpkg/DESCRIPTION’ ... OK\nE> * preparing ‘invalidpkg’:\nE> * checking DESCRIPTION meta-information ... ERROR\nE> Malformed Depends or Suggests or Imports or Enhances field.\nE> Offending entries:\nE>   testthat\nE> foobar\nE> Entries must be names of packages optionally followed by '<=' or '>=',\nE> white space, and a valid version number in parentheses.\nE> \nE> See section 'The DESCRIPTION file' in the 'Writing R Extensions'\nE> manual.\nE> "
  Backtrace:
    1. testthat::expect_error(...)
    6. remotes:::safe_build_package(...)
    7. pkgbuild::build(...)
   10. pkgbuild::rcmd_build_tools(...)
   12. callr::rcmd_safe(...)
   13. callr:::run_r(options)
   15. base::with.default(...)
   16. [ base::eval(...) ] with 1 more call
   22. throw(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 396 | SKIPPED: 78 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: safe_build_package fails appropriately with pkgbuild (@test-install.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
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’,
    ‘R_GlobalContext’

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:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rphast.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.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [31s/73s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library('testthat')
  > test_check("spocc")
  Loading required package: spocc
  ── 1. Failure: has_coords works with all data sources as planned (@test-has_coor
  anyNA(dd$inat$data[[1]]$longitude) isn't false.
  
  ── 2. Failure: has_coords works with all data sources as planned (@test-has_coor
  anyNA(dd$inat$data[[1]]$latitude) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 120 | SKIPPED: 10 | WARNINGS: 4 | FAILED: 2 ]
  1. Failure: has_coords works with all data sources as planned (@test-has_coords.R#44) 
  2. Failure: has_coords works with all data sources as planned (@test-has_coords.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ 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/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [34s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  ── 1. Failure: opfw - coverage  (@test_opwf.R#69)  ─────────────────────────────
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests 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.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is 73.1Mb
  sub-directories of 1Mb or more:
    gdal   3.9Mb
    libs  68.8Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  24.0Mb
Package suggested but not available for checking: 'REBayes'
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 3.6.2 (2019-12-12) -- "Dark and Stormy Night"
Copyright (C) 2019 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  6.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.0Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running 'testthat.R' [107s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bayes4psy)
  Loading required package: Rcpp
  > 
  > test_check("bayes4psy")
  -- 1. Error: reaction_time compare_distributions two fits  ---------------------
  result would be too long a vector
  Backtrace:
   1. bayes4psy::compare_distributions(fit1, fit2 = fit2)
   2. bayes4psy::compare_distributions(fit1, fit2 = fit2)
   3. bayes4psy:::difference(...)
   6. mcmcse::mcse(diff_smaller)
   7. base::sapply(...)
   8. base::lapply(X = X, FUN = FUN, ...)
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: reaction_time compare_distributions two fits 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 134.1Mb
  sub-directories of 1Mb or more:
    include  133.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BinQuasi.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running examples in 'blscrapeR-Ex.R' failed
The error most likely occurred in:

> ### Name: qcew_api
> ### Title: Request data from the Quarterly Census of Employment and Wages.
> ### Aliases: qcew_api
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> # A request for the employment levels and wages for NIACS 5112: Software Publishers.
> dat <- qcew_api(year=2017, qtr="a", slice="industry", sliceCode=5112)
Please set a numeric year.
Trying BLS servers...
URL caused a warning. Please check your parameters and try again: https://data.bls.gov/cew/data/api/2017/a/industry/5112.csv
Error in qcew_api(year = 2017, qtr = "a", slice = "industry", sliceCode = 5112) : 
  object 'qcewDat' not found
Execution halted
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
    lib      50.6Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Cairo.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ClimDown.Rcheck/00install.out' for details.
Running examples in 'clustermole-Ex.R' failed
The error most likely occurred in:

> ### Name: read_gmt
> ### Title: Read a GMT file into a data frame
> ### Aliases: read_gmt
> 
> ### ** Examples
> 
> gmt <- "http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt"
> gmt_tbl <- read_gmt(gmt)
Warning in file(con, "r") : InternetOpenUrl failed: ''
Error in file(con, "r") : cannot open the connection
Calls: read_gmt -> strsplit -> readLines -> file
Execution halted
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustermole)
  > 
  > test_check("clustermole")
  -- 1. Error: read_gmt() output (@test-functions.R#103)  ------------------------
  cannot open the connection
  Backtrace:
   1. clustermole::read_gmt(file = "http://software.broadinstitute.org/gsea/msigdb/supplemental/scsig.all.v1.0.symbols.gmt")
   3. base::readLines(file)
   4. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: read_gmt() output (@test-functions.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'colorspace-Ex.R' failed
The error most likely occurred in:

> ### Name: scale_colour_continuous_diverging
> ### Title: HCL-Based Continuous Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_continuous_diverging
> ###   scale_color_continuous_diverging scale_fill_continuous_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
> 
> # generate dataset and base plot
> set.seed(100)
> df <- data.frame(country = LETTERS, V = runif(26, -40, 40))
> df$country = factor(LETTERS, LETTERS[order(df$V)]) # reorder factors
> gg <- ggplot(df, aes(x = country, y = V, fill = V)) +
+   geom_bar(stat = "identity") +
+   labs(y = "Under/over valuation in %", x = "Country") +
+   coord_flip() + theme_minimal()
>   
> # plot with default diverging scale
> gg + scale_fill_continuous_diverging()
Error in if (!alpha || all(lab_in[, 4] == 1)) { : 
  missing value where TRUE/FALSE needed
Calls: scale_fill_continuous_diverging ... <Anonymous> -> ggproto -> <Anonymous> -> colour_ramp
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.0Mb
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: create_env
> ### Title: Create your conda virtual env with DALEX
> ### Aliases: create_env
> 
> ### ** Examples
> 
> if(DALEXtra:::is_conda()) {
+   create_env(system.file("extdata", "testing_environment.yml", package = "DALEXtra"))
+ } else {
+   "conda is required"
+ }
Error: lexical error: invalid char in json text.
                                       NA
                     (right here) ------^
Execution halted
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:11959 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DFA.CANCOR.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
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:11423 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11423 (sockconn)
Execution halted
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:11138 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11138 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DistributionOptimization.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
    libs   1.2Mb
Running examples in 'EcoHydRology-Ex.R' failed
The error most likely occurred in:

> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Warning in file(con, "r") : InternetOpenUrl failed: 'XÂ'
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error(s) in re-building vignettes:
--- re-building 'ezpickr_vignette.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://codecov.io/gh/jooyoungseo/ezpickr/branch/master/graph/badge.svg
HttpExceptionRequest Request {
  host                 = "codecov.io"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/gh/jooyoungseo/ezpickr/branch/master/graph/badge.svg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HostCannotConnect "codecov.io" [connect: failed (Connection timed out (WSAETIMEDOUT))]))
Error: processing vignette 'ezpickr_vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'ezpickr_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/FastRWeb.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/fdANOVA.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'vignette.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Quitting from lines 162-168 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
infinite or missing values in 'x'
--- failed re-building 'vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/fdrDiscreteNull.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is 84.7Mb
  sub-directories of 1Mb or more:
    L8NY18   2.3Mb
    gdal     3.9Mb
    libs    72.1Mb
    proj     5.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Error(s) in re-building vignettes:
--- re-building 'intro.Rnw' using knitr
--- finished re-building 'intro.Rnw'

--- re-building 'parallel.Rnw' using knitr
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "parallel.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.6.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.2/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'parallel.Rnw' failed with diagnostics:
Failed to locate the 'texi2pdf' output file (by engine 'knitr::knitr') for vignette with name 'parallel'. The following files exist in directory '.': 'brref.bib', 'intro.R', 'intro.Rnw', 'intro.aux', 'intro.bbl', 'intro.blg', 'intro.log', 'intro.out', 'intro.pdf', 'intro.tex', 'intro.toc', 'parallel.R', 'parallel.Rnw', 'parallel.tex'
--- failed re-building 'parallel.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/GRANBase.Rcheck/00install.out' for details.
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/r-reticulate/python.exe" "d:/RCompile/CRANpkg/lib/3.6/reticulate/config/config.py"' had status 2

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

Probably some imports need to be declared in the NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'ashg2012.Rnw' using Sweave
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.6.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.2/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'ashg2012.Rnw' failed with diagnostics:
running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-36\unhbox\voidb@x \penalty \@M \ {}1.
2/share/texmf/tex/latex/Sweave.sty' not found.

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

--- failed re-building 'ashg2012.Rnw'

SUMMARY: processing the following file failed:
  'ashg2012.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is 130.5Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
Running examples in 'hail-Ex.R' failed
The error most likely occurred in:

> ### Name: hail_hydra
> ### Title: Read HYDRA data
> ### Aliases: hail_hydra
> 
> ### ** Examples
> 
> # Simple exmaple
> walmart_data <- hail_hydra("Walmart Eco Roof")
Warning in file(con, "r") : InternetOpenUrl failed: ''
Error in file(con, "r") : cannot open the connection
Calls: hail_hydra -> hydra_base -> readLines -> file
Execution halted
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hail)
  > 
  > test_check("hail")
  -- 1. Error: hail_hydra works (@test.R#4)  -------------------------------------
  cannot open the connection
  Backtrace:
   1. hail::hail_hydra("Walmart Eco Roof")
   2. hail:::hydra_base(station_data$urls, station_data$stations)
   3. base::readLines(url)
   4. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: hail_hydra works (@test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'highcharter-Ex.R' failed
The error most likely occurred in:

> ### Name: get_data_from_map
> ### Title: Helper function to get the data inside the map data The urls are
> ###   listed in <URL: https://code.highcharts.com/mapdata/>.
> ### Aliases: get_data_from_map
> 
> ### ** Examples
> 
> dta <- download_map_data("https://code.highcharts.com/mapdata/countries/us/us-ca-all.js")
trying URL 'https://code.highcharts.com/mapdata/countries/us/us-ca-all.js'
Warning in download.file(url, tmpfile) : InternetOpenUrl failed: ''
Error in download.file(url, tmpfile) : 
  cannot open URL 'https://code.highcharts.com/mapdata/countries/us/us-ca-all.js'
Calls: download_map_data -> download.file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Hmisc.Rcheck/00install.out' for details.
Running examples in 'horizon-Ex.R' failed
The error most likely occurred in:

> ### Name: horizonSearch
> ### Title: Horizon elevation angle from DEM RasterLayer
> ### Aliases: horizonSearch
> 
> ### ** Examples
> 
> r <- getData('alt', country='ALB')
trying URL 'https://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Warning in utils::download.file(url = aurl, destfile = fn, method = "auto",  :
  InternetOpenUrl failed: ''
Error in utils::download.file(url = aurl, destfile = fn, method = "auto",  : 
  cannot open URL 'https://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Calls: getData -> .raster -> .download -> <Anonymous>
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.4Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.7Mb
Running examples in 'iRefR-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_MITAB_to_edgeList
> ### Title: Convert MITAB format to edgeList format
> ### Aliases: convert_MITAB_to_edgeList
> 
> ### ** Examples
> 
>      ## get tables
>      irefindex_curr_ecoli = get_irefindex("562", "13.0", tempdir())
Downloading iRefIndex file...
trying URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Warning in download.file(url, destfile = zipfile) :
  InternetOpenUrl failed: ''
Error in download.file(url, destfile = zipfile) : 
  cannot open URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Calls: get_irefindex -> download.file
Execution halted
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] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11383 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11383 (sockconn)
Execution halted
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:11468 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11468 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/jackalope.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/JavaGD.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
Package unavailable to check Rd xrefs: 'REBayes'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.6Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/MTPS.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'muHVT.Rmd' using rmarkdown
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/R.oo_1.23.0.zip'
Content type 'application/zip' length 967752 bytes (945 KB)
==========================================
downloaded 808 KB

Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 827392 != reported length 967752
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/R.methodsS3_1.7.1.zip'
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'R.methodsS3' failed
trying URL 'http://cran.us.r-project.org/bin/windows/contrib/3.6/R.utils_2.9.2.zip'
Content type 'application/zip' length 1410519 bytes (1.3 MB)
===========================================
downloaded 1.2 MB

Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1241088 != reported length 1410519
Warning in unzip(zipname, exdir = dest) :
  error 1 in extracting from zip file
Warning in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'R.oo/DESCRIPTION', probable reason 'No such file or directory'
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'muHVT.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/mvtnorm.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'NEArender_vignette.Rmd' using rmarkdown
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 174-175 (NEArender_vignette.Rmd) 
Error: processing vignette 'NEArender_vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building 'NEArender_vignette.Rmd'

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

Error: Vignette re-building failed.
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 'd:/Rcompile/CRANpkg/local/3.6/NestedCategBayesImpute.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/NetworkChange.Rcheck/00install.out' for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.0Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
Running examples in 'norris-Ex.R' failed
The error most likely occurred in:

> ### Name: get_joke_categories
> ### Title: Get all available joke categories from ICNDB
> ### Aliases: get_joke_categories
> 
> ### ** Examples
> 
> get_joke_categories()
Error: lexical error: invalid char in json text.
                                       <!DOCTYPE html> <html lang="en-
                     (right here) ------^
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.6Mb
    libs   2.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   1.9Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
  -- 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: cannot open URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
  Class:   simpleError/error/condition
  Backtrace:
   1. testthat::expect_error(quickSetupOxcal(), NA)
   6. oxcAAR::quickSetupOxcal()
   7. oxcAAR:::downloadOxcal(path = path)
   8. utils::download.file(...)
  
  -- 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  -- 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  == testthat results  ===========================================================
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests 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) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
trying URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
cannot open URL 'https://c14.arch.ox.ac.uk/OxCalDistribution.zip'
--- 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  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  13.2Mb
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:11144 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11144 (sockconn)
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/phateR.Rcheck/00install.out' for details.
Running 'testthat.R' [99s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("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
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  -- 1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102)  ---------
  not implemented for objects of class sfc_GEOMETRYCOLLECTION
  Backtrace:
    1. plotly::plot_ly()
    8. plotly::add_sf(...)
    9. plotly:::to_basic.GeomSf(dat)
   12. plotly:::fortify_sf(d[[i]])
   14. sf:::st_coordinates.sfc(model$geometry)
  
  == testthat results  ===========================================================
  [ OK: 1370 | SKIPPED: 45 | WARNINGS: 74 | FAILED: 1 ]
  1. Error: plot_ly() defaults to blank axes (@test-plotly-sf.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/PPRL.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   3.1Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(quickmatch)
  Loading required package: distances
  Please cite the `quickmatch` package as:
     Savje, Fredrik, Michael J. Higgins and Jasjeet S. Sekhon (2017),
     "Generalized Full Matching", arXiv 1703.03882.
     https://arxiv.org/abs/1703.03882
  > 
  > test_check("quickmatch")
  -- 1. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#240)
  `quickmatch(my_distances, my_data$treatment)` did not produce any warnings.
  
  -- 2. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#241)
  `expect_identical(...)` did not produce any warnings.
  
  -- 3. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#243)
  `quickmatch(my_distances, my_data$treatment, secondary_unassigned_method = "closest_seed")` did not throw an error.
  
  == testthat results  ===========================================================
  [ OK: 599 | SKIPPED: 0 | WARNINGS: 43 | FAILED: 3 ]
  1. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#240) 
  2. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#241) 
  3. Failure: `quickmatch` handles discrete covariates (@test_quickmatch.R#243) 
  
  Error: testthat unit tests failed
  Execution halted
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/R2GUESS.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'raincpc_demo.Rmd' using knitr
Loading required package: sp
Quitting from lines 50-52 (raincpc_demo.Rmd) 
Error: processing vignette 'raincpc_demo.Rmd' failed with diagnostics:
Raw file from CPC doesnt exist! First run cpc_get_rawdata()!
--- failed re-building 'raincpc_demo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd.rsp' using rsp
Warning in parseRepos(sets = repos, where = where, fallback = fallback,  :
  Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: '@CRAN@' -> 'http://cran.r-project.org'
also installing the dependencies 'highr', 'markdown', 'xfun'

Warning in download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.r-project.org/bin/windows/contrib/3.6/highr_0.8.zip'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'highr' failed
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 57344 != reported length 190038
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 49152 != reported length 181812
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1273856 != reported length 1430729
Warning in unzip(zipname, exdir = dest) :
  error 1 in extracting from zip file
Warning in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'markdown/DESCRIPTION', probable reason 'No such file or directory'

Error: processing vignette 'introduction.Rmd.rsp' failed with diagnostics:
cannot open the connection
--- failed re-building 'introduction.Rmd.rsp'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd.rsp' using rsp
Warning in parseRepos(sets = repos, where = where, fallback = fallback,  :
  Had to fall back to a set of predefined repositories (please make sure to set your package repositories properly, cf. ?setRepositories): CRAN: '@CRAN@' -> 'http://cran.r-project.org'
also installing the dependencies 'highr', 'markdown', 'xfun'

Warning in download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'http://cran.r-project.org/bin/windows/contrib/3.6/highr_0.8.zip'
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package 'highr' failed
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 45056 != reported length 190038
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 12288 != reported length 181812
Warning in download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1241088 != reported length 1430729
Warning in unzip(zipname, exdir = dest) :
  error 1 in extracting from zip file
Warning in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'markdown/DESCRIPTION', probable reason 'No such file or directory'

Error: processing vignette 'introduction.Rmd.rsp' failed with diagnostics:
cannot open the connection
--- failed re-building 'introduction.Rmd.rsp'

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rblpapi.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.3Mb
    libs      2.0Mb
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
Running 'testthat.R' [24s]
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")
  -- 1. Error: getParkIDs returns the right results (@test-getParkIDs.R#2)  ------
  cannot open the connection
  Backtrace:
   1. retrosheet::getParkIDs()
   2. base::scan(u, nlines = 1L, nmax = 2L, what = "", sep = ",", quiet = TRUE)
   3. base::file(file, "r")
  
  == testthat results  ===========================================================
  [ OK: 30 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: getParkIDs returns the right results (@test-getParkIDs.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rglpk.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmagic.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(roundhouse)
  > 
  > test_check("roundhouse")
  -- 1. Error: random_fact() works (@test-all.R#4)  ------------------------------
  API did not return json
  Backtrace:
   1. roundhouse::random_fact(n = 1L, include = NULL, exclude = NULL)
  
  -- 2. Error: fetch_categories() works (@test-all.R#10)  ------------------------
  API did not return json
  Backtrace:
   1. roundhouse::fetch_categories()
  
  -- 3. Error: kick() works (@test-all.R#19)  ------------------------------------
  API did not return json
  Backtrace:
   1. roundhouse::kick()
   3. roundhouse::random_fact()
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: random_fact() works (@test-all.R#4) 
  2. Error: fetch_categories() works (@test-all.R#10) 
  3. Error: kick() works (@test-all.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    1.7Mb
    tests   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
Found the following significant warnings:
   #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/3.6/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/i386/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 'd:/Rcompile/CRANpkg/lib/3.6/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/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
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.
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:  3.4 0.11 3.51 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 21.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    libs  17.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rstap.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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/3.6/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/3.6/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
Running 'lint.R' [1s]
  Running 'spelling.R' [0s]
  Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  -- 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  lexical error: invalid char in json text.
                                         NA
                       (right here) ------^
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy_env()
   4. reticulate::conda_list(conda = "auto")
   5. jsonlite::fromJSON(conda_envs)
   6. jsonlite:::parse_and_simplify(...)
   7. jsonlite:::parseJSON(txt, bigint_as_char)
   8. jsonlite:::parse_string(txt, bigint_as_char)
  
  == testthat results  ===========================================================
  [ OK: 1 | SKIPPED: 50 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/spatialfusion.Rcheck/00install.out' for details.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.2Mb
Running 'testthat.R' [85s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  > test_check("spocc")
  Loading required package: spocc
  -- 1. Failure: occ2df works when eventDate gone - another eg (@test-occ2df.R#44)
  Names of `outdf` ('name', 'longitude', 'latitude', 'prov', 'key') don't match 'name', 'longitude', 'latitude', 'prov', 'key', 'date'
  
  == testthat results  ===========================================================
  [ OK: 100 | SKIPPED: 14 | WARNINGS: 24 | FAILED: 1 ]
  1. Failure: occ2df works when eventDate gone - another eg (@test-occ2df.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/stringi.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
    0.0     0.0     2.4 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11141 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.02    0.00    2.11 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11188 (sockconn)
Execution halted
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/tth.Rcheck/00install.out' for details.
Running examples in 'uklr-Ex.R' failed
The error most likely occurred in:

> ### Name: uklr_def
> ### Title: Linked Data Definitions
> ### Aliases: uklr_def ukhp_def ukppd_def uktrans_def
> 
> ### ** Examples
> 
> 
> uklr_def()
Warning in file(file, "rt") : InternetOpenUrl failed: ''
Error in file(file, "rt") : cannot open the connection
Calls: uklr_def -> read.csv -> read.table -> file
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.3Mb
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") : InternetOpenUrl failed: ''
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

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

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

> ### Name: webuse
> ### Title: webuse
> ### Aliases: webuse webuselist webuse-package
> 
> ### ** Examples
> 
> webuse("auto")
`curl` package not installed, falling back to using `url()`
Warning in open.connection(con, "rb") : InternetOpenUrl failed: ''
Error in open.connection(con, "rb") : cannot open the connection
Calls: webuse ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("webuse")
  > 
  > test_check("webuse")
  -- 1. Error: Basic functionality (@tests.R#5)  ---------------------------------
  cannot open the connection
  Backtrace:
    1. testthat::expect_true(...)
    5. webuse::webuse("auto")
    6. haven::read_dta(...)
    7. readr::datasource(file)
    8. readr:::datasource_connection(file, skip, skip_empty_rows, comment)
    9. readr:::read_connection(path)
   11. base::open.connection(con, "rb")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Basic functionality (@tests.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > library("wyz.code.metaTesting")
  > test_check("wyz.code.metaTesting")
  -- 1. Failure: opfw - coverage  (@test_opwf.R#69)  -----------------------------
  `createWrapperFunction(myfun, c("x_d", "y_i", "z_c", "t_d"))` produced no output
  
  == testthat results  ===========================================================
  [ OK: 477 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: opfw - coverage  (@test_opwf.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/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) and/or pandoc-citeproc 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

Warning in normalizePath(f2) :
  path[1]="webshot3f472895632b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3f472895632b.png': No such file or directory
Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adamethods.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapt_demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'adapt_demo.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adapt_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'WGCNA', 'DeconRNASeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ade4TkGUI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘amigaDiskFiles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'amigaDiskFiles.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘amigaDiskFiles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adiv.Rcheck/00install.out’ for details.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘adpss_ex.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'adpss_ex.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adpss_ex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/afCEC.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘afpt-aerodynamic-model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'afpt-aerodynamic-model.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-aerodynamic-model.Rmd’

--- re-building ‘afpt-basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'afpt-basic-usage.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-basic-usage.Rmd’

--- re-building ‘afpt-multiple-birds.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'afpt-multiple-birds.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-multiple-birds.Rmd’

SUMMARY: processing the following files failed:
  ‘afpt-aerodynamic-model.Rmd’ ‘afpt-basic-usage.Rmd’
  ‘afpt-multiple-birds.Rmd’

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

> ### Name: baker.wheat.uniformity
> ### Title: Uniformity trial of wheat
> ### Aliases: baker.wheat.uniformity
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(baker.wheat.uniformity)
> dat <- baker.wheat.uniformity
> 
> require(desplot)
Loading required package: desplot
Error: package or namespace load failed for ‘desplot’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
> desplot(yield ~ col*row, dat,
+         flip=TRUE, aspect=1,
+         main="baker.wheat.uniformity")
Error in desplot(yield ~ col * row, dat, flip = TRUE, aspect = 1, main = "baker.wheat.uniformity") : 
  could not find function "desplot"
Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'agridat_data.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_examples.Rmd’

--- re-building ‘agridat_papadakis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'agridat_papadakis.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_papadakis.Rmd’

SUMMARY: processing the following files failed:
  ‘agridat_data.Rmd’ ‘agridat_examples.Rmd’ ‘agridat_papadakis.Rmd’

Error: Vignette re-building failed.
Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
--- 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: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AIG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggseas’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/akmedoids.Rcheck/00install.out’ for details.
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/alphashape3d.Rcheck/00install.out’ for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata  11.4Mb
No protocol specified
No protocol specified
Error(s) in re-building vignettes:
  ...
--- re-building ‘amen.Rnw’ using knitr
Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/animalTrack.Rcheck/00install.out’ for details.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.1Mb
Package suggested but not available for checking: ‘rhdf5’
Running ‘testthat.R’ [80s/128s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 381 SKIPPED: 0 FAILED: 25
  1. Error: h5 : processing correctBalance when mcYear is set to NULL (@test-correctBalance.R#72) 
  2. Error: h5 : processing correctBalance when mcYear is set to 1 (@test-correctBalance.R#108) 
  3. Error: h5 : processing correctBalance when mcYear is set to 1 for weekly or monthly data (@test-correctBalance.R#146) 
  4. Error: h5 : processing correctBalance when mcYear is set to 1 for monthly data on districts (@test-correctBalance.R#227) 
  5. Error: h5 : processing correctBalance with addProcessingH5 (@test-correctBalance.R#273) 
  6. Error: h5 : processing, write results (@test-h5_processing.R#4) 
  7. Error: h5 : processing, write results mcAll (@test-h5_processing.R#30) 
  8. Error: h5 : all data (@test-h5_processing.R#56) 
  9. Error: h5 : processing calc by user (@test-h5_processing.R#72) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Anthropometry.Rcheck/00install.out’ for details.
installed size is 163.3Mb
  sub-directories of 1Mb or more:
    libs  162.9Mb
Packages suggested but not available for checking: 'Biostrings', 'kebabs'
Packages suggested but not available for checking:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice'
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/aqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/archiDART.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘argparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘argparse.Rrst’

SUMMARY: processing the following file failed:
  ‘argparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Arothron.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  22.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  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/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/audio.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Packages required but not available:
  'org.Hs.eg.db', 'ConsensusClusterPlus', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/babel.Rcheck/00install.out’ for details.
Running examples in ‘babette-Ex.R’ failed
The error most likely occurred in:

> ### Name: prepare_file_creation
> ### Title: Prepare for 'BEAST2' creating files
> ### Aliases: prepare_file_creation
> 
> ### ** Examples
> 
> library(testthat)
> 
> # For a test inference model, the files can be prepared
> inference_model <- create_test_inference_model()
> beast2_options <- create_beast2_options()
> expect_silent(prepare_file_creation(inference_model, beast2_options))
Error in prepare_file_creation(inference_model, beast2_options) : 
  Cannot create file '/Users/urbanek/Library/Caches/beast2_162d0747c3ebd.xml.state'. 
Maybe no permissions to write there?
Calls: expect_silent ... withCallingHandlers -> withVisible -> eval_bare -> prepare_file_creation
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BACA.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   2.8Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 68.0Mb
  sub-directories of 1Mb or more:
    libs  67.0Mb
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bagRboostR.Rcheck/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘philr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALCONY.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALLI.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ArrayExpress’
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bapred.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.0Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr

Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAwiR.Rcheck/00install.out’ for details.
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bayesCL.Rcheck/00install.out’ for details.
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  12.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  17.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  13.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BayesXsrc.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.1Mb
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BClustLonG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DNAcopy’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bcROCsurface.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/beadarrayFilter.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanz_vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
cannot open the connection
--- failed 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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
installed size is 131.4Mb
  sub-directories of 1Mb or more:
    include  131.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.4Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BIGL.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshotb1974e6b49f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb1974e6b49f.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.7Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bioacoustics.Rcheck/00install.out’ for details.
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BiocStyle', 'BiocVersion'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Biocomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiodiversityR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bios2mds.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiSEp.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'gRain'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 335.2Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      326.4Mb
installed size is 75.9Mb
  sub-directories of 1Mb or more:
    libs  75.4Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bootsPLS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
Running examples in ‘Boptbd-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphoptBbd
> ### Title: Creates the graphical layout of resultant optimal design
> ### Aliases: graphoptBbd
> ### Keywords: Graphical layout
> 
> ### ** Examples
> 
>     ##To create the graphical layout of the D-optimal block design
>     ##obtained using the treatment exchange algorithm for 
>     trt.N <- 10  #Number of treatments
>     blk.N <- 10  #Number of blocks
>     alpha <- 0.1 #alpha value 
>     beta  <- 0.1 #beta value 
>     OptdesF <- rbind(1:10, c(2:10,1)) #Bayesian A-optimal block design (loop design)
> 
>     graphoptBbd(trt.N = 10, blk.N = 10, alpha = 0.1, beta = 0.1, OptdesF, Optcrit = "A")
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graphoptBbd ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bpca.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
No protocol specified

(R:60058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainKCCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainR.Rcheck/00install.out’ for details.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.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 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Running examples in ‘breathteststan-Ex.R’ failed
The error most likely occurred in:

> ### Name: stan_fit
> ### Title: Bayesian Stan fit to 13C Breath Data
> ### Aliases: stan_fit
> 
> ### ** Examples
> 
> library(breathtestcore)
> suppressPackageStartupMessages(library(dplyr))
> d = breathtestcore::simulate_breathtest_data(n_records = 3) # default 3 records
> data = breathtestcore::cleanup_data(d$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 120, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = "m")$m), beta = as.vector(rstan::extract(fit, permuted = TRUE, 
         pars = "beta")$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = "k")$k))
  3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 7 FAILED: 2
  1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16) 
  2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘grid’ ‘qpdf’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'vsn', 'DESeq2', 'pasilla'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Brundle.Rcheck/00install.out’ for details.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  27.8Mb
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.3Mb
File ‘Buddle/libs/Buddle.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘cppMain.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  8.5Mb
  sub-directories of 1Mb or more:
    article   2.0Mb
    libs      4.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
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) and/or pandoc-citeproc 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 object is masked from 'package:dplyr':

    %>%

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

    grid, legend

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.
Warning in normalizePath(f2) :
  path[1]="webshot17f0e554a7ebc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17f0e554a7ebc.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

No protocol specified
Running examples in ‘cairoDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cairo
> ### Title: The Cairo Graphics Device
> ### Aliases: Cairo Cairo_pdf Cairo_ps Cairo_svg Cairo_png
> ### Keywords: device
> 
> ### ** Examples
> 
> Cairo()

(R:61668): Gdk-CRITICAL **: gdk_screen_get_width: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_width_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_height: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_height_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:61668): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:61668): Gtk-CRITICAL **: gtk_window_set_default_size: assertion `width >= -1' failed

(R:61668): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:61668): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:61668): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: Cairo()
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'
Package unavailable to check Rd xrefs: ‘GenomicRanges’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
Package required and available but unsuitable version: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Package unavailable to check Rd xrefs: ‘limma’
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")
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: stat.DESeq ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘CaRpools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc 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 in normalizePath(f2) :
  path[1]="webshot87bf53b79c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot87bf53b79c.png': No such file or directory
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.2Mb
installed size is 120.7Mb
  sub-directories of 1Mb or more:
    libs  120.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Package suggested but not available for checking: ‘graph’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.9Mb
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/changepoint.np.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pbdMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ChaosGame.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘multtest’
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
--- failed re-building ‘Visualising_Interactions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ComplexHeatmap’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
Running ‘testthat.R’ [63s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    0.023   0.004   0.027 
  
  
  g object size: 4.2 Mb
  Passing results to tmle.
  	Estimating missingness mechanism 
  1.4 Mb
  0.5 Mb
  9.1 Mb
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: (unknown) (@test-gen_superlearner.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CleanBSequences.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-79 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
--- failed re-building ‘getstarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clpAPI.Rcheck/00install.out’ for details.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clusterSim.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Package unavailable to check Rd xrefs: ‘Biobase’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'InteractionSet', 'GenomicInteractions',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.4Mb
Package suggested but not available for checking: ‘limma’
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) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Epi
Quitting from lines 36-38 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted