Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘cplexAPI’
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
Error in re-building vignettes:
  ...
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 327-331 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
unused arguments ("Group 1", 4, 7)
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
Execution halted
Package suggested but not available for checking: ‘gifski’
Error in re-building vignettes:
  ...
Warning in engine$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
Loading required package: foreach
Loaded glmnet 2.0-16
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
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] 12795 - 6398 == 6398
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.6Mb
    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 in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in grep("\n", x) : input string 14 is invalid in this locale
Warning in grep("^(---|\\.\\.\\.)\\s*$", lines) :
  input string 14 is invalid in this locale
Warning in grepl(chunk.begin, lines) :
  input string 14 is invalid in this locale
Warning in grepl(chunk.end, lines) :
  input string 14 is invalid in this locale
Quitting from lines 2-22 (GxE_testing.Rmd) 
Error: processing vignette 'GxE_testing.Rmd' failed with diagnostics:
invalid multibyte string, element 1
Execution halted
Running ‘testthat.R’ [72s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lgr)
  > 
  > test_check("lgr")
  ── 1. Failure: multiprocess: Logging works (@test_parallel.R#43)  ──────────────
  readLines\(tf\)\[\[5\]\] does not match "child.*flapply 1".
  Actual value: "INFO  \[2019-03-13 05:15:39\.194\] child flapply 2"
  
  ── 2. Failure: multiprocess: Logging works (@test_parallel.R#44)  ──────────────
  readLines\(tf\)\[\[6\]\] does not match "child.*flapply 2".
  Actual value: "INFO  \[2019-03-13 05:15:39\.242\] child flapply 1"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 420 SKIPPED: 6 FAILED: 2
  1. Failure: multiprocess: Logging works (@test_parallel.R#43) 
  2. Failure: multiprocess: Logging works (@test_parallel.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Running ‘testthat.R’ [171s/197s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  ── 1. Failure: grid_terrain return the same both with LAScatalog and LAS (@test-
  mean(error) not equal to 0.048.
  1/1 mismatches
  [1] NA - 0.048 == NA
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 571 SKIPPED: 0 FAILED: 1
  1. Failure: grid_terrain return the same both with LAScatalog and LAS (@test-grid_terrain.R#107) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: interactive_text_explanations
> ### Title: Interactive explanations
> ### Aliases: interactive_text_explanations text_explanations_output
> ###   render_text_explanations
> 
> ### ** Examples
> 
> library(text2vec)
> library(xgboost)
Error in library(xgboost) : there is no package called ‘xgboost’
Execution halted
Running ‘testthat.R’ [16s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lime)
  > 
  > test_check("lime")
  
  H2O is not running yet, starting it now...
  
  Note:  In case of errors look at the following log files:
      /tmp/RtmpZZaGLW/h2o_ripley_started_from_r.out
      /tmp/RtmpZZaGLW/h2o_ripley_started_from_r.err
  
  java version "1.7.0_65"
  Java(TM) SE Runtime Environment (build 1.7.0_65-b17)
  Java HotSpot(TM) Server VM (build 24.65-b04, mixed mode)
  
  Starting H2O JVM and connecting: ... Connection successful!
  
  R is connected to the H2O cluster: 
      H2O cluster uptime:         5 seconds 484 milliseconds 
      H2O cluster timezone:       Europe/London 
      H2O data parsing timezone:  UTC 
      H2O cluster version:        3.22.1.1 
      H2O cluster version age:    2 months and 12 days  
      H2O cluster name:           H2O_started_from_R_ripley_vcm448 
      H2O cluster total nodes:    1 
      H2O cluster total memory:   0.89 GB 
      H2O cluster total cores:    16 
      H2O cluster allowed cores:  16 
      H2O cluster healthy:        TRUE 
      H2O Connection ip:          localhost 
      H2O Connection port:        54321 
      H2O Connection proxy:       NA 
      H2O Internal Security:      FALSE 
      H2O API Extensions:         AutoML, Algos, Core V3, Core V4 
      R Version:                  R version 3.5.3 Patched (2019-03-11 r76219) 
  
  ── 1. Error: (unknown) (@test-text.R#3)  ───────────────────────────────────────
  there is no package called 'xgboost'
  1: library(xgboost) at testthat/test-text.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 18 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-text.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-224 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'xgboost'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R          1.8Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/lmSubsets.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.4Mb
Package suggested but not available for checking: ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 62-63 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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 0.6-3
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: The job for model 'model' exited abnormally with the error message: Incorrect input to omxRowSortHelper: 0 1 0 9
Execution halted
Running examples in ‘MachineShop-Ex.R’ failed
The error most likely occurred in:

> ### Name: XGBModel
> ### Title: Extreme Gradient Boosting Models
> ### Aliases: XGBModel XGBDARTModel XGBLinearModel XGBTreeModel
> 
> ### ** Examples
> 
> modelfit <- fit(Species ~ ., data = iris, model = XGBTreeModel())
Loading required namespace: xgboost
Failed with error:  ‘there is no package called ‘xgboost’’
Error in requireModelNamespaces(model@packages) : 
  install required packages: xgboost
Calls: fit ... fit.ModelFrame -> .fit -> .fit.MLModel -> requireModelNamespaces
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  ‘av’ ‘rsvg’ ‘tesseract’ ‘gifski’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Quitting from lines 228-237 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Magick: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4354
Execution halted
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot3442622a4d86.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3442622a4d86.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
Packages required but not available: ‘CausalImpact’ ‘bsts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Error in re-building vignettes:
  ...
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 (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Quitting from lines 39-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unable to start device 'png'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/meanr.Rcheck/00install.out’ for details.
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: BCG
> ### Title: Dataset on the Effectiveness of the BCG Vaccine for Preventing
> ###   Tuberculosis
> ### Aliases: BCG
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(BCG)
> 
> ## Univariate meta-analysis on the log of the odds ratio
> summary( meta(y=ln_OR, v=v_ln_OR, data=BCG,
+               x=cbind(scale(Latitude,scale=FALSE),
+               scale(Year,scale=FALSE))) )

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

Traceback:
 1: runHelper(model, frontendStart, intervals, silent, suppressWarnings,     unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
 2: mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(mxRun(mx.model, intervals = FALSE, suppressWarnings = suppressWarnings,     silent = silent, ...), error = function(e) e)
 7: meta(y = y, v = v, data = my.df, model.name = "No predictor",     suppressWarnings = TRUE, silent = TRUE)
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(meta(y = y, v = v, data = my.df, model.name = "No predictor",     suppressWarnings = TRUE, silent = TRUE), error = function(e) e)
12: meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE)))
13: summary(meta(y = ln_OR, v = v_ln_OR, data = BCG, x = cbind(scale(Latitude,     scale = FALSE), scale(Year, scale = FALSE))))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 32-40 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
    libs   1.7Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: line 411: 12220 Killed                  "$@" 2>&5 1>&2
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Packages suggested but not available for checking: ‘REBayes’ ‘Rmosek’
Packages unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Packages suggested but not available for checking:
  ‘minfi’ ‘IlluminaHumanMethylation450kmanifest’
Package suggested but not available for checking: ‘FSelector’
Error in re-building vignettes:
  ...
Warning in engine$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 5-183 (./toc/vignettetoc.Rmd) 
Quitting from lines 5-183 (./toc/vignettetoc.Rmd) 
Error: processing vignette 'a_1_getting_started.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Packages suggested but not available for checking:
  ‘FSelector’ ‘RWeka’ ‘xgboost’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.4Mb
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
Package which this enhances but not available for checking: ‘MonetDBLite’
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running ‘test-all.R’ [65s/78s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  ── 1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(tf, quiet = TRUE) at testthat/test_mudata.io.R:554
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 967 SKIPPED: 0 FAILED: 1
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/multinet.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: geometry
Loading required package: rootSolve
Warning in engine$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 252-268 (munsellinterpol-guide.Rmd) 
Error: processing vignette 'munsellinterpol-guide.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
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    2.5Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(temp_file_path) at testthat/test-unname_all_chunks.R:22
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running examples in ‘ncdump-Ex.R’ failed
The error most likely occurred in:

> ### Name: NetCDF
> ### Title: Information about a NetCDF file, in convenient form.
> ### Aliases: NetCDF
> 
> ### ** Examples
> 
> rnc <- NetCDF(system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package= "ncdump"))
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(x) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
Calls: NetCDF -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncdump)
  > 
  > test_check("ncdump")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@testbasic.r#6)  ───────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
  1: NetCDF(ifile) at testthat/testbasic.r:6
  2: ncdf4::nc_open(x)
  3: stop(paste("Error in nc_open trying to open file", filename))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testbasic.r#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ncmeta-Ex.R’ failed
The error most likely occurred in:

> ### Name: nc_att
> ### Title: NetCDF attributes
> ### Aliases: nc_att nc_att.NetCDF nc_att.character
> 
> ### ** Examples
> 
> f <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
> nc_att(f, 0, 0)
Error: NetCDF: HDF error
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 2.2-2 (2019-03-07) 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 www.image.ucar.edu/~nychka/Fields for
 a vignette and other supplements. 
> 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
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  8.3Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10007 milliseconds with 0 out of 0 bytes received
Execution halted
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    CppCode   1.3Mb
    R         6.9Mb
    include   5.4Mb
    tests     1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Package suggested but not available for checking: ‘DDD’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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 'walkthrough.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.03 0.036 0.449
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
Running examples in ‘norm2-Ex.R’ failed
The error most likely occurred in:

> ### Name: emNorm
> ### Title: EM algorithm for incomplete multivariate normal data
> ### Aliases: emNorm emNorm.default emNorm.formula emNorm.norm
> ### Keywords: multivariate NA
> 
> ### ** Examples
> 
> ## run EM for marijuana data with strict convergence criterion
> data(marijuana)
> result <- emNorm(marijuana, criterion=1e-06)

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

Traceback:
 1: emNorm.default(marijuana, criterion = 1e-06)
 2: emNorm(marijuana, criterion = 1e-06)
An irrecoverable exception occurred. R is aborting now ...
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 in re-building vignettes:
  ...
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
Execution halted
Running examples in ‘noteMD-Ex.R’ failed
The error most likely occurred in:

> ### Name: note_in_html
> ### Title: Print text input in html
> ### Aliases: note_in_html
> 
> ### ** Examples
> 
> note_in_html("Please write note using **Markdown** syntax! ")
sh: +RTS:  not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-42 (downloading_data_nsrr.Rmd) 
Error: processing vignette 'downloading_data_nsrr.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 2-30 (NumeroGuide.rmd) 
Error: processing vignette 'NumeroGuide.rmd' failed with diagnostics:
could not find function "pkg_ver"
Execution halted
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.0Mb
    doc    1.7Mb
    help   2.4Mb
Packages suggested but not available for checking: ‘RMark’ ‘R2ucare’
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     3.5Mb
    models   4.6Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  Element-wise '+' not conformable: 'OneFactor1.R arg 0' is 0x0 and 'OneFactor1.U' is 5x5
OneFactor1.R arg 0 =  matrix(c(    # 0x0), byrow=TRUE, nrow=0, ncol=0)
OneFactor1.U =  matrix(c(    # 5x5
 0.0407325,   0,   0,   0,   0
,   0, 0.0379439,   0,   0,   0
,   0,   0, 0.0407455,   0,   0
,   0,   0,   0, 0.0393083,   0
,   0,   0,   0,   0, 0.0362145), byrow=TRUE, nrow=5, ncol=5)
Calls: mxRun -> runHelper
Execution halted

 *** caught segfault ***
address 8, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Error in re-building vignettes:
  ...
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 'Introduction.Rmd' failed with diagnostics:
invalid multibyte string at '<f0><9f><95><9b></h2>

<p><strong>OptimClassifier</strong> provides a set of tools for creating models, selecting the best parameters combination for a model, and select the best threshold for your binary classification. The package contains tools for:</p>

<ul>
<li>Linear Model (LM) </li>
<li>Generalized Linear Model (GLM) </li>
<li>Linear Mixed Model (LMM) </li>
<li>Classification And Regression Tree (CART)</li>
<li>Discriminant Analysis (DA)</li>
<li>Neural Networks (NN)</li>
<li>Support Vector Machines (SVM)</li>
</ul>

<h2>Take a quick look at functions</h2>

<p>The main function could summarize in this table:</p>

<style type="text/css">
table td {padding: 0px 0px;border-width: 1px; border-style: inset;}
.tg  {border-collapse:collapse;border-spacing:0;}
.tg {border-style:solid;padding: 0px  0px; border-width:1px; overflow:hidden;word-break:normal;border-color:black;}
.tgd{border-style:soli
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  7.3Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/osqp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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'
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
  
  ── 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 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 in re-building vignettes:
  ...
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
Execution halted
Running examples in ‘P2C2M-Ex.R’ failed
The error most likely occurred in:

> ### Name: p2c2m.complete
> ### Title: Execute the complete P2C2M pipeline via a single command
> ### Aliases: p2c2m.complete
> 
> ### ** Examples
> 
> ## Example of the minimal data requirements to run P2C2M
> 
> # The absolute path to the input directory is set
> inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
> 
> # The name of the xml-file generated by BEAUTi and located in 
> # "inPath" is set
> inFile <- "sim.E.003.small.xml"
> 
> # Posterior predictive simulations with a setting of 2 simulation 
> # replicates are preformed
> sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
Error in python.exec(code, get.exception) : cannot import name izip
Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
Error in re-building vignettes:
  ...
Warning in engine$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 23-68 (advancedFeatures.Rmd) 
Error: processing vignette 'advancedFeatures.Rmd' failed with diagnostics:
there is no package called 'xgboost'
Execution halted
Running ‘testthat.R’ [30s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(parglm)
  > 
  > test_check("parglm")
  ── 1. Failure: works with different families w/ starting values (@test_parglm_fa
  gaussian_inverse_FAST w/ weigths not equal to f2[to_check].
  Component "residuals": Mean relative difference: 5.183904e-07
  
  ── 2. Failure: works with different families w/ starting values (@test_parglm_fa
  gaussian_inverse_FAST w/ weigths not equal to s2[!names(s2) %in% excl].
  Component "deviance.resid": Mean relative difference: 1.204083e-06
  
  
  error: chol(): decomposition failed
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1319 SKIPPED: 0 FAILED: 2
  1. Failure: works with different families w/ starting values (@test_parglm_fams.R#220) 
  2. Failure: works with different families w/ starting values (@test_parglm_fams.R#220) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    doc       1.4Mb
    extdata   9.8Mb
installed size is  6.3Mb
  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  6.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.2Mb
Packages required but not available: ‘MSnbase’ ‘mzR’

Package suggested but not available for checking: ‘faahKO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/phenofit.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_POS_tag_documents.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#5)  ───────────────
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_extract_phrases.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#5) 
  2. Error: See if extractor works (@test_extract_phrases.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics:
there is no package called 'quanteda'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
Running examples in ‘phylocomr-Ex.R’ failed
The error most likely occurred in:

> ### Name: ph_aot
> ### Title: aot
> ### Aliases: ph_aot
> 
> ### ** Examples
> 
> traits_file <- system.file("examples/traits_aot", package = "phylocomr")
> phylo_file <- system.file("examples/phylo_aot", package = "phylocomr")
> 
> # from data.frame
> traitsdf_file <- system.file("examples/traits_aot_df",
+   package = "phylocomr")
> traits <- read.table(text = readLines(traitsdf_file), header = TRUE,
+   stringsAsFactors = FALSE)
> phylo_str <- readLines(phylo_file)
> (res <- ph_aot(traits, phylo = phylo_str))
Error: Program '/home/ripley/R/Lib32/phylocomr/bin//phylocom' terminated by SIGNAL (Segmentation Fault)
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   2.0Mb
    doc    3.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
* installing *source* package ‘baseballstats’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (baseballstats)

* installing *source* package ‘sartre’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (sartre)

* installing *source* package ‘milne’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (milne)

* installing *source* package ‘pkgnet’ ...
** package ‘pkgnet’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pkgnet)
Quitting from lines 77-113 (pkgnet-intro.Rmd) 
Error: processing vignette 'pkgnet-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    htmlwidgets   3.0Mb
Running examples in ‘plotly-Ex.R’ failed
The error most likely occurred in:

> ### Name: partial_bundle
> ### Title: Use a partial bundle of plotly.js
> ### Aliases: partial_bundle
> 
> ### ** Examples
> 
> 
> # ----------------------------------------------------------------------
> # This function is always safe to use when rendering a single 
> # plotly graph. In this case, we get a 3x file reduction.
> # ----------------------------------------------------------------------
> 
> library(plotly)
> p <- plot_ly(x = 1:10, y = 1:10) %>% add_markers()
> save_widget <- function(p, f) {
+   owd <- setwd(dirname(f))
+   on.exit(setwd(owd))
+   htmlwidgets::saveWidget(p, f)
+   mb <- round(file.info(f)$size / 1e6, 3)
+   message("File is: ", mb," MB")
+ }
> f1 <- tempfile(fileext = ".html")
> f2 <- tempfile(fileext = ".html")
> save_widget(p, f1)
Error in htmlwidgets::saveWidget(p, f) : 
  Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Calls: save_widget -> <Anonymous>
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Package suggested but not available for checking: ‘enviGCMS’
Error in re-building vignettes:
  ...
Warning in engine$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 115-119 (globalstd.Rmd) 
Error: processing vignette 'globalstd.Rmd' failed with diagnostics:
there is no package called 'enviGCMS'
Execution halted
Running ‘testthat.R’ [60s/84s]
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] 3 - 0 == 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1561 SKIPPED: 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 in re-building vignettes:
  ...
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 139-140 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   2.8Mb
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
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test-all.R’ [8s/11s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
  ── 1. Failure: fastLik(C++) vs algebraic lik (@test-lik.R#63)  ─────────────────
  likPOUMMGivenTreeVTipsC(...) not equivalent to dVTipsGivenTreePOUMMg0Alg(...).
  1/1 mismatches
  [1] -1988554 - -3204 == -1985351
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: fastLik(C++) vs algebraic lik (@test-lik.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot2d313d397d03.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2d313d397d03.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘Rmosek’
Error in re-building vignettes:
  ...
Warning in engine$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 46-49 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-44 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           6.6Mb
    help          2.2Mb
    htmlwidgets   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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: edeaR
Loading required package: eventdataR
Loading required package: processmapR
Loading required package: xesreadR
Loading required package: processmonitR
Loading required package: petrinetR

Attaching package: 'bupaR'

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

    filter

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

    timestamp

Quitting from lines 23-49 (use-external-data-to-change-tokens.Rmd) 
Error: processing vignette 'use-external-data-to-change-tokens.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
Found the following significant warnings:
  Warning: replacing previous import ‘loo::kfold’ by ‘rstanarm::kfold’ when loading ‘psycho’
See ‘/home/ripley/R/packages/tests32/psycho.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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
rstanarm (Version 2.18.2, packaged: 2018-11-08 22:19:38 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().

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: replacing previous import 'loo::kfold' by 'rstanarm::kfold' when loading 'psycho'
Warning in R2_LOO_Adjusted(fit) :
  Something went wrong in the Loo-adjusted R2 computation.
Warning: There were 9 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Markov chains did not converge! Do not analyze results!

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 506-534 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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    R      1.9Mb
    data   1.0Mb
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    help   1.0Mb
installed size is  5.4Mb
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    doc        4.8Mb
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installed size is  7.3Mb
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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  5.5Mb
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    data   3.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.3Mb
    libs      1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-35 (quadmesh.Rmd) 
Error: processing vignette 'quadmesh.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘stm’
Installation failed.
See ‘/home/ripley/R/packages/tests32/quanteda.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is  6.5Mb
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    data   2.1Mb
    doc    3.7Mb
installed size is  5.6Mb
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    data      2.3Mb
    extdata   1.5Mb
installed size is 14.2Mb
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    api           3.0Mb
    htmlwidgets   9.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Execution halted
Running ‘testthat.R’ [194s/262s]
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: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/RtmpgeaWe6/file7426751c761f/2_2': no such file or directory
  ── 1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#
  [ENOENT] Failed to stat '/tmp/RtmpgeaWe6/file7426751c761f/2_2': no such file or directory
  
  1: randomsearch(fun = fun, max.evals = 10000, max.execbudget = 4, target.fun.value = target.fun.value) at testthat/test_randomsearch.R:83
  2: randomsearch.smoof_function(fun = fun, max.evals = 10000, max.execbudget = 4, target.fun.value = target.fun.value)
  3: parallelMap(wrap.fun2, seq_len(par.jobs), level = "randomsearch.feval", simplify = FALSE)
  4: checkResultsAndStopWithErrorsMessages(res)
  5: stopWithJobErrorMessages(inds, vcapply(result.list[inds], as.character))
  6: stopf("Errors occurred in %i slave jobs, displaying at most 10 of them:\n\n%s\n%s", 
         n, collapse(msgs, sep = "\n"), extra.msg)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 69 SKIPPED: 0 FAILED: 1
  1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘rapidraker-Ex.R’ failed
The error most likely occurred in:

> ### Name: rapidrake
> ### Title: Rapid RAKE
> ### Aliases: rapidrake
> 
> ### ** Examples
> 
> rapidrake(txt = "some text that has great keywords")
Error in .jfindClass(as.character(class)) : 
  java.lang.UnsupportedClassVersionError: opennlp/tools/stemmer/snowball/SnowballStemmer : Unsupported major.minor version 52.0
Calls: rapidrake ... <Anonymous> -> <Anonymous> -> jclassName -> .jfindClass
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rapidraker)
  > 
  > test_check("rapidraker")
  ── 1. Error: (unknown) (@test-rapidrake.R#3)  ──────────────────────────────────
  no field, method or inner class called 'handled' 
  1: test_that("rapidrake works for non-atomic, non-empty char vectors", {
         out <- rapidrake(slowraker::dog_pubs$abstract[1:10])
         expect_equal(length(out), 10)
     }) at testthat/test-rapidrake.R:3
  2: test_code(desc, code, env = parent.frame())
  3: tryCatch(withCallingHandlers({
         eval(code, test_env)
         if (!handled && !is.null(test)) {
             skip_empty()
         }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
         message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) {
     })
  4: tryCatchList(expr, classes, parentenv, handlers)
  5: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], 
         parentenv, handlers[[nh]])
  6: doTryCatch(return(expr), name, parentenv, handler)
  7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, "handled")
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-rapidrake.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R   2.6Mb
Packages suggested but not available for checking:
  ‘playwith’ ‘rggobi’ ‘xgboost’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.1Mb
    etc    2.2Mb
    po     1.5Mb
Running examples in ‘raustats-Ex.R’ failed
The error most likely occurred in:

> ### Name: abs_search
> ### Title: Search dataset information from the ABS.Stat API
> ### Aliases: abs_search
> 
> ### ** Examples
> 
>  ## ABS dataset search
>  x <- abs_search(pattern = "consumer price index")
>  x <- abs_search(pattern = "census")
>  x <- abs_search(pattern = "labour force")
> 
>  ## ABS indicator search
>  x <- abs_search(pattern = "all groups", dataset="CPI")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: abs_search ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
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: readxl
Attaching package: 'raustats'
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Dec%202018?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Dec%202018?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/6401.0Dec%202018?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/5206.0Dec%202018?OpenDocument
Quitting from lines 697-698 (raustats_introduction.Rmd) 
Error: processing vignette 'raustats_introduction.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
installed size is  5.0Mb
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    doc    2.4Mb
    libs   1.7Mb
Running examples in ‘rbi.helpers-Ex.R’ failed
The error most likely occurred in:

> ### Name: DIC
> ### Title: Compute Deviance Information Criterion (DIC) for a libbi model
> ### Aliases: DIC DIC.libbi
> 
> ### ** Examples
> 
> example_run <- bi_read(system.file(package="rbi", "example_output.nc"))
Error in R_nc4_open: NetCDF: HDF error
Error in nc_open(tools::file_path_as_absolute(x)) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
Calls: bi_read -> bi_open -> nc_open
Execution halted
Running examples in ‘rbi-Ex.R’ failed
The error most likely occurred in:

> ### Name: attach_data
> ### Title: Attach a new file or data set to a 'libbi' object
> ### Aliases: attach_data attach_data.libbi
> 
> ### ** Examples
> 
> bi <- libbi(model = system.file(package="rbi", "PZ.bi"))
> example_output <- bi_read(system.file(package="rbi", "example_output.nc"))
Error in R_nc4_open: NetCDF: HDF error
Error in nc_open(tools::file_path_as_absolute(x)) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
Calls: bi_read -> bi_open -> nc_open
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rbi)
  
  Attaching package: 'rbi'
  
  The following objects are masked from 'package:stats':
  
      filter, optimise, predict, simulate, update
  
  The following object is masked from 'package:utils':
  
      fix
  
  The following object is masked from 'package:base':
  
      sample
  
  > 
  > test_check("rbi")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@test-samples.r#4)  ────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
  1: bi_read(system.file(package = "rbi", "example_output.nc")) at testthat/test-samples.r:4
  2: bi_open(x)
  3: nc_open(tools::file_path_as_absolute(x))
  4: stop(paste("Error in nc_open trying to open file", filename))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 145 SKIPPED: 6 FAILED: 1
  1. Error: (unknown) (@test-samples.r#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 23.4Mb
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    cont  23.4Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons. Currently only supports Font Awesome 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
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    data   5.1Mb
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    doc   3.5Mb
    po    2.2Mb
Running ‘testthat.R’ [4s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Error: (unknown) (@test_deputados.R#81)  ─────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ── 2. Error: (unknown) (@test_proposicoes.R#91)  ───────────────────────────────
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ── 3. Error: (unknown) (@test_votacoes.R#70)  ──────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
Execution halted
installed size is  8.3Mb
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    corpora   8.2Mb
installed size is  6.4Mb
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    include   5.1Mb
Error in re-building vignettes:
  ...
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:
Python shared library not found, Python bindings not loaded.
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 23.9Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    include   6.6Mb
Running ‘testthat.R’ [19s/23s]
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] 15456 - 15453 == 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: csf algorithm works (@test-CSF.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [16s/337s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  ── 1. Error: DEFRA server should be running (@test-metadata.R#13)  ─────────────
  HTTP/2 stream 5 was not closed cleanly: CANCEL (err 8)
  1: httr::GET(url = "http://uk-air.defra.gov.uk", path = "networks/find-sites", query = list(site_name = site_name, 
         pollutant = pollutant, group_id = group_id, closed = closed, country_id = country_id, 
         region_id = region_id, location_type = location_type, search = "Search+Network", 
         view = "advanced", action = "results")) at testthat/test-metadata.R:13
  2: request_perform(req, hu$handle$handle)
  3: request_fetch(req$output, req$url, handle)
  4: request_fetch.write_memory(req$output, req$url, handle)
  5: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20 SKIPPED: 1 FAILED: 1
  1. Error: DEFRA server should be running (@test-metadata.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   2.6Mb
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   1.2Mb
    doc    3.0Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(readtext)
  > library(quanteda)
  Error in library(quanteda) : there is no package called 'quanteda'
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: quanteda
Quitting from lines 146-152 (readtext_vignette.Rmd) 
Error: processing vignette 'readtext_vignette.Rmd' failed with diagnostics:
could not find function "corpus"
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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.
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’
Error in re-building vignettes:
  ...
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 296-299 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
Error in the HTTP2 framing layer
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
Running ‘restfulr_unit_tests.R’
Running the tests in ‘tests/restfulr_unit_tests.R’ failed.
Complete output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Timing stopped at: 0.262 0.019 0.526
  Error : Internal Server Error
  
  Timing stopped at: 0.045 0.003 0.112
  Error : Internal Server Error
  
  
  
  RUNIT TEST PROTOCOL -- Thu Mar  7 01:08:54 2019 
  *********************************************** 
  Number of test functions: 3 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  restfulr RUnit Tests - 3 test functions, 2 errors, 0 failures
  ERROR in test_RestContainer_CRUD: Error : Internal Server Error
  
  ERROR in test_RestUri_CRUD: Error : Internal Server Error
  
  
  Test files with failing tests
  
     test_RestContainer.R 
       test_RestContainer_CRUD 
  
     test_RestUri.R 
       test_RestUri_CRUD 
  
  
  Error in testPackage("restfulr") : unit tests failed for package restfulr
  Calls: <Anonymous> -> testPackage
  Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

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

> ### Name: baseline_corr
> ### Title: Bidimensional baseline correction
> ### Aliases: baseline_corr
> 
> ### ** Examples
> 
> library(colorRamps)
> chrom_name <- system.file("extdata", "08GB.cdf", package = "RGCxGC")
> chrom_2D <- read_chrom(chrom_name, 5L)
Error: NetCDF: HDF error
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (Explanation.Rmd) 
Error: processing vignette 'Explanation.Rmd' failed with diagnostics:
NetCDF: HDF error
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.6Mb
    libs    1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$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.
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
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.3Mb
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
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.
Running examples in ‘RJDemetra-Ex.R’ failed
The error most likely occurred in:

> ### Name: count
> ### Title: Count the number of objects inside a workspace or
> ###   multiprocessing
> ### Aliases: count
> 
> ### ** Examples
> 
> wk <- new_workspace()
Error in .jcall("ec/tstoolkit/jdr/ws/Workspace", "Lec/tstoolkit/jdr/ws/Workspace;",  : 
  RcallMethod: cannot determine object class
Calls: new_workspace -> .jcall
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Error in re-building vignettes:
  ...
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: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.8.6 [Built: 2019-02-23 08:23:56 UTC]
A luminescence lab staff member to its customer: 'Tell me the age, I tell you the price.'

Attaching package: 'RLumModel'

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

    model_LuminescenceSignals

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 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    examples   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
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 11.1Mb
  sub-directories of 1Mb or more:
    R  11.1Mb
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘illuminaHumanv3.db’
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
Running examples in ‘rosr-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_eq
> ### Title: Create a demo equation sheet
> ### Aliases: create_eq
> 
> ### ** Examples
> 
> create_eq(tempdir())
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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'
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 in re-building vignettes:
  ...
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: moonBook
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

Loading required package: ggplot2
Quitting from lines 68-69 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    help   4.1Mb
Running ‘rsolr_unit_tests.R’ [1m/180m]
Running the tests in ‘tests/rsolr_unit_tests.R’ failed.
Complete output:
  > rsolr:::.test()
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  
  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, colMeans, colSums, colnames,
      dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
      intersect, is.unsorted, lapply, lengths, mapply, match, mget,
      order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
      rowMeans, rowSums, 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 in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  
  There were 50 or more warnings (use warnings() to see the first 50)
  Timing stopped at: 31.94 16.64 1.074e+04
  Error in file() : cannot open the connection
  Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> portIsOpen -> file
  In addition: Warning message:
  In file() :
    cannot open file '/tmp/Rtmpyaaieb/Rf22119b93354': Too many open files
  Execution halted
Error in re-building vignettes:
  ...
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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


Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  10.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs        6.6Mb
    unitTests   1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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 17-22 (minimal-rstan-package.Rmd) 
Error: processing vignette 'minimal-rstan-package.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
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)
2019-03-11 04:13:44 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.36.252).
2019-03-11 04:13:44 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2019-03-11 04:13:44 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")
2019-03-11 04:13:44 WARNING:rsuite:Project environment is not locked!
2019-03-11 04:13:44 INFO:rsuite:Exporting project from /tmp/RtmpQPa4kl/example_16574fb07bc/my_project ...
2019-03-11 04:13:44 INFO:rsuite:Exporting project from /tmp/RtmpQPa4kl/example_16574fb07bc/my_project ... done
2019-03-11 04:13:44 WARNING:rsuite:Zip building aborted for /tmp/RtmpQPa4kl/prjpack_my_project_1.0x.zip
2019-03-11 04:13:44 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
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    rmarkdown   4.9Mb
Error in re-building vignettes:
  ...
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 block_exec(params) :
  Failed to tidy R code in chunk 'pkg_data'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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

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

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'st_books_wiki2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

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

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

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

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

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

Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
R: Fatal IO error 146 (Connection refused) on X server :5.0.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    sample_data   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    example   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/SCCI.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
Packages suggested but not available for checking: ‘flowMerge’ ‘flowClust’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   1.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
    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 ...
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 18, 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 ...
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc     11.6Mb
    sqlite   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 216-219 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Error in re-building vignettes:
  ...
Warning in engine$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 26-42 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running ‘testthat.R’ [6s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smapr)
  > 
  > test_check("smapr")
  ── 1. Error: Incorrect credentials cause a 401 error (@test-zzz.R#23)  ─────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: httr::GET(handle = tmp_handle, config = httr::authenticate("fakeuser", "fakepass")) at testthat/test-zzz.R:23
  2: request_perform(req, hu$handle$handle)
  3: request_fetch(req$output, req$url, handle)
  4: request_fetch.write_memory(req$output, req$url, handle)
  5: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 33 FAILED: 1
  1. Error: Incorrect credentials cause a 401 error (@test-zzz.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘SmartEDA-Ex.R’ failed
The error most likely occurred in:

> ### Name: ExpReport
> ### Title: Function to create HTML EDA report
> ### Aliases: ExpReport
> 
> ### ** Examples
> 
> # Overview of the data
> ExpReport(mtcars,Template=NULL,Target=NULL,label=NULL,op_file="Myreport.html",
+ op_dir=getwd(),sc=2,sn=2,Rc=NULL)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
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 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
Execution halted
Running examples in ‘SMCP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SMCP
> ### Title: Smoothed minimax concave penalization (SMCP) method for
> ###   genome-wide association studies.
> ### Aliases: SMCP sp
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> x=matrix(rnorm(100*20),100,20)
> y=rnorm(100)
> fit=SMCP(x,y,0.3,0.3,3)
> #solution path for this data
> s.p=sp(x,y,0.3,10,0.05,3)
Error in SMCP(x, y, alpha, delta * i, gamma) : 
  NA/NaN/Inf in foreign function call (arg 6)
Calls: sp -> SMCP
Execution halted
Running ‘testthat.R’ [174s/210s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.4.1 loaded.
  This is package "smooth", v2.4.7
  > 
  > 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: 77 SKIPPED: 0 FAILED: 1
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [14s/172s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(soilDB)
  Loading required package: aqp
  This is aqp 1.17
  
  Attaching package: 'aqp'
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > 
  > 
  > 
  > test_check("soilDB")
  Error in open.connection(con, "rb") : 
    Timeout was reached: Resolving timed out after 10000 milliseconds
  ── 1. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
  class\(x\.extended\) does not match "list".
  Actual value: "NULL"
  
  ── 2. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.
  class\(x\.extended\$SPC\) does not match "SoilProfileCollection".
  Actual value: "NULL"
  
  ── 3. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchO
  names(x.extended) not equal to c(...).
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 139 SKIPPED: 2 FAILED: 3
  1. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#26) 
  2. Failure: fetchOSD() returns a list + SPC in extended mode (@test-fetchOSD.R#27) 
  3. Failure: fetchOSD() returns reasonable data in extended mode (@test-fetchOSD.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 5.67 secs
Identifing all possible orderings..
Total run time: 2.99 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running ‘test-all.R’ [300s/450s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
    Using cached copy of .inputObjects event in test module.   
  ── 1. Failure: simulation runs with simInit and spades (@test-simulation.R#86)  
  mySim$caribou$x not equivalent to `pos_x`.
  100/100 mismatches (average diff: 9.83)
  [1]   3.67 -   1.06 ==   2.613
  [2]  43.57 -  44.45 ==  -0.883
  [3]  47.23 -  45.88 ==   1.351
  [4]   3.60 -  -1.32 ==   4.918
  [5]  20.23 -  17.86 ==   2.370
  [6] -47.81 -  48.48 == -96.294
  [7]  16.55 -  10.75 ==   5.796
  [8] -21.41 - -24.63 ==   3.218
  [9] -47.28 - -48.51 ==   1.234
  ...
  
  ── 2. Failure: simulation runs with simInit and spades (@test-simulation.R#87)  
  mySim$caribou$y not equivalent to `pos_y`.
  100/100 mismatches (average diff: 5.15)
  [1] -15.00 - -15.90 ==  0.898
  [2]  -5.35 -  -8.97 ==  3.616
  [3]  19.51 -  25.27 == -5.758
  [4] -36.40 - -39.07 ==  2.674
  [5] -33.64 - -32.96 == -0.678
  [6]  15.57 -  19.59 == -4.027
  [7]  15.12 -  14.87 ==  0.249
  [8]  39.63 -  38.26 ==  1.368
  [9]  -6.33 -  -8.17 ==  1.831
  ...
  
    Using cached copy of .inputObjects event in child6 module.   
    Using memoised copy of .inputObjects event in child6 module
    Using memoised copy of .inputObjects event in child6 module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 458 SKIPPED: 32 FAILED: 2
  1. Failure: simulation runs with simInit and spades (@test-simulation.R#86) 
  2. Failure: simulation runs with simInit and spades (@test-simulation.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'SpaDES.core'

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

    end, start

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

    citation

Loading required package: SpaDES.tools
Loading required package: RandomFields
Loading required package: sp
Loading required package: RandomFieldsUtils

Attaching package: 'RandomFields'

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

    RFoptions

Setting:
  options(
    spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    reproducible.cachePath = '/tmp/RtmpYgaipa/reproducible/cache'
    spades.inputPath = '/tmp/Rtmpc4aqWc/SpaDES/inputs'
    spades.outputPath = '/tmp/Rtmpc4aqWc/SpaDES/outputs'
    spades.modulePath = '/home/ripley/R/Lib32/SpaDES.core/sampleModules'
  )
Quitting from lines 376-382 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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

Quitting from lines 249-254 (SparseIndexTracking-vignette.Rmd) 
Error: processing vignette 'SparseIndexTracking-vignette.Rmd' failed with diagnostics:
The engine "block2" is for R Markdown only
Execution halted
installed size is  5.1Mb
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Error in re-building vignettes:
  ...
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$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
Execution halted
installed size is  7.3Mb
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installed size is 15.9Mb
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    nc    3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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 185-187 (stars1.Rmd) 
Error: processing vignette 'stars1.Rmd' failed with diagnostics:
failed to open 'x', value given was: "/home/ripley/R/Lib32/stars/nc/bcsd_obs_1999.nc"
Execution halted
Package required but not available: ‘stm’

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

Package suggested but not available for checking: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
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    datasets   2.7Mb
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Error in re-building vignettes:
  ...
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
Execution halted
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    doc    2.5Mb
installed size is  7.5Mb
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installed size is  5.9Mb
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Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 1f0, cause 'memory not mapped'

Traceback:
 1: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
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  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
Error in re-building vignettes:
  ...
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
Execution halted
installed size is  6.4Mb
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    data   1.5Mb
    doc    3.9Mb
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
Package unavailable to check Rd xrefs: ‘tesseract’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.7Mb
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Packages suggested but not available for checking: ‘quanteda’ ‘stm’
Error in re-building vignettes:
  ...
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'
Execution halted
Error in re-building vignettes:
  ...
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 block_exec(params) :
  Failed to tidy R code in chunk 'ex1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: sp
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'ex7'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'map1_tiles'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'map1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 208-214 (tiler.Rmd) 
Error: processing vignette 'tiler.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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    doc         3.9Mb
    rmarkdown   1.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    doc       2.9Mb
    extdata   8.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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'
Execution halted
installed size is  6.4Mb
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    doc   4.9Mb
Error in re-building vignettes:
  ...
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: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
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    fonts   5.3Mb
installed size is  6.5Mb
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    doc    1.2Mb
    libs   4.7Mb
Error in re-building vignettes:
  ...
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'
Execution halted
installed size is  5.2Mb
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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 FAILED: 1
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc         5.5Mb
    dummydata   1.5Mb
    libs        1.9Mb
Package suggested but not available for checking: ‘TSstudio’
Error in re-building vignettes:
  ...
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

Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
there is no package called 'TSstudio'
Execution halted
Error in re-building vignettes:
  ...
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
Execution halted
installed size is  8.9Mb
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    doc   8.2Mb
installed size is 15.6Mb
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    data  14.9Mb
installed size is 29.8Mb
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    data  29.1Mb
installed size is  7.3Mb
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    extdata   6.4Mb
Running examples in ‘utiml-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctrl
> ### Title: CTRL model for multi-label Classification
> ### Aliases: ctrl
> 
> ### ** Examples
> 
> model <- ctrl(toyml, "RANDOM")
Error in ctrl(toyml, "RANDOM") : 
  There are no installed package 'FSelector' to use CTRL multi-label classifier
Execution halted
Running ‘testthat.R’ [21s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Error: CTRL (@test_brclassifiers.R#94)  ──────────────────────────────────
  There are no installed package 'FSelector' to use CTRL multi-label classifier
  1: ctrl(train, "RANDOM") at testthat/test_brclassifiers.R:94
  2: stop(paste("There are no installed package 'FSelector' to use CTRL", "multi-label classifier"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1120 SKIPPED: 21 FAILED: 1
  1. Error: CTRL (@test_brclassifiers.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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 123-126 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.0Mb
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    R      3.8Mb
    doc    1.3Mb
    help   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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 169-173 (introduction_to_vimp.Rmd) 
Error: processing vignette 'introduction_to_vimp.Rmd' failed with diagnostics:
there is no package called 'xgboost'
Execution halted
installed size is 12.1Mb
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    doc           5.7Mb
    htmlwidgets   4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  "predict.c", line 111: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.3Mb
installed size is 12.5Mb
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    doc  12.3Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
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    client  10.1Mb
    doc      1.1Mb
installed size is 12.7Mb
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    doc  12.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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 78-81 (wikisourcer.Rmd) 
Error: processing vignette 'wikisourcer.Rmd' failed with diagnostics:
HTTP error 404.
Execution halted
installed size is  7.6Mb
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    bn   7.5Mb
installed size is  5.8Mb
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    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [57s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("workflowr")
  This is workflowr version 1.2.0
  Run ?workflowr for help getting started
  > 
  > test_check("workflowr")
  NA
  ── 1. Error: wflow_use_github can be used post GitLab (@test-wflow_use_github.R#
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: wflow_publish(file.path(s$analysis, "*Rmd"), view = FALSE, project = path) at testthat/test-wflow_use_github.R:54
  2: wflow_build(files = files_to_build, make = FALSE, update = update, republish = republish, 
         view = view, clean_fig_files = TRUE, delete_cache = delete_cache, seed = seed, 
         local = FALSE, verbose = verbose, dry_run = dry_run, project = project)
  3: build_rmd_external(f, seed = seed, log_dir = log_dir, verbose = verbose, envir = .GlobalEnv)
  4: tryCatch(callr::r_safe(build_rmd, args = list(rmd, seed, ...), stdout = stdout_file, 
         stderr = stderr_file, show = verbose), error = function(e) {
         message(wrap("Build failed. See log files for full details."))
         message("stdout: ", stdout_file)
         message("stderr: ", stderr_file)
         stdout_lines <- readLines(stdout_file)
         n <- length(stdout_lines)
         cat(stdout_lines[pmax(1, n - 10):n], sep = "\n")
         stop(e$message, call. = FALSE)
     })
  5: tryCatchList(expr, classes, parentenv, handlers)
  6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7: value[[3L]](cond)
  8: stop(e$message, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 838 SKIPPED: 116 FAILED: 1
  1. Error: wflow_use_github can be used post GitLab (@test-wflow_use_github.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
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    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
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.
Installation failed.
See ‘/home/ripley/R/packages/tests32/xgboost.Rcheck/00install.out’ for details.
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
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found
Error in base::system(cmd, intern = TRUE) : 
  error in running command: 'Illegal seek'
Calls: findJulia -> testJSON -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
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: 'xspliner'

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

    xspline

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Welcome to DALEX (version: 0.2.7).
Cannot extract model family. Use gaussian.
Cannot extract model link. Use identity.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-32 (cases.Rmd) 
Error: processing vignette 'cases.Rmd' failed with diagnostics:
there is no package called 'xgboost'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 818-843 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
(converted from warning) Removed 4070 rows containing missing values (geom_raster).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Welcome to package ztable ver 0.2.0
Warning in engine$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 103-108 (ztable_update.Rmd) 
Error: processing vignette 'ztable_update.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
In addition: Warning message:
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
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [22s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  ── 1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  dim(df1) not equal to c(4, 16).
  1/2 mismatches
  [1] 5 - 4 == 1
  
  ── 2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$linf[3] not equivalent to 87.4.
  1/1 mismatches
  [1] 75.1 - 87.4 == -12.3
  
  ── 3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$k[2] not equivalent to 0.15.
  1/1 mismatches
  [1] 0.53 - 0.15 == 0.38
  
  ── 4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$locality[1] not equivalent to "Central Adriatic, 100-200 m depth".
  1/1 mismatches
  x[1]: "northeast Mediterranean Sea"
  y[1]: "Central Adriatic, 100-200 m depth"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 193 SKIPPED: 1 FAILED: 4
  1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#6) 
  2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#7) 
  3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#8) 
  4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  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.
Found the following significant warnings:
  mcmc.c:337:4: 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/BayHap.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [30s/35s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-biglm.R#7)  ──────────────────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(am ~ mpg, mtcars, family = binomial()) at testthat/test-biglm.R:7
  2: bigglm(am ~ mpg, mtcars, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 904 SKIPPED: 2 FAILED: 1
  1. Error: (unknown) (@test-biglm.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7f11e2154b50, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/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]
  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.
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:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/epanet2toolkit.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:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 124-148 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
Execution halted
Running ‘testthat.R’ [32s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: Test that create_stack creates tmx if requested (@test-create_CRU
  raster::maxValue(CRU_stack_list[[1]][[1]]) not equal to 12.9.
  1/1 mismatches
  [1] 12.9 - 12.9 == 3.81e-07
  
  ── 2. Failure: Test that create_stack creates tmn if requested (@test-create_CRU
  raster::maxValue(CRU_stack_list[[1]][[1]]) not equal to 4.3.
  1/1 mismatches
  [1] 4.3 - 4.3 == 1.91e-07
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 493 SKIPPED: 23 FAILED: 2
  1. Failure: Test that create_stack creates tmx if requested (@test-create_CRU_stack.R#868) 
  2. Failure: Test that create_stack creates tmn if requested (@test-create_CRU_stack.R#1233) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:276:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:331:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:156:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:164:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:205:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/haven.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’ [1s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  ── 1. Error: (unknown) (@test-hurdat.R#4)  ─────────────────────────────────────
  Timeout was reached: Connection timed out after 10000 milliseconds
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip, skip_empty_rows = skip_empty_rows)
  7: datasource_connection(file, skip, skip_empty_rows, comment)
  8: read_connection(path)
  9: open(con, "rb")
  10: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [38s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(huxtable)
  > 
  > 
  > we_are_in_R_CMD_check <- TRUE
  > test_check("huxtable")
  ── 1. Failure: Data written in appropriate format (@test-openxlsx.R#101)  ──────
  `openxlsx::saveWorkbook(wb, file = "test-xlsx.xlsx", overwrite = TRUE)` produced messages.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 889 SKIPPED: 57 FAILED: 1
  1. Failure: Data written in appropriate format (@test-openxlsx.R#101) 
  
  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:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: 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:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: 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.
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: 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/MonetDBLite.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [68s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  ── 1. Failure: covex-E (@test_covex.R#54)  ─────────────────────────────────────
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 1.01 - 1.07 == -0.0586
  1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 174 SKIPPED: 2 FAILED: 1
  1. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 49-52 (geocode.Rmd) 
Error: processing vignette ‘geocode.Rmd’ failed with diagnostics:
cannot open the connection to 'https://geodata.nationaalgeoregister.nl/locatieserver/v3/free?fq=type:adres&q=Martinikerkhof%203&rows=1'
Execution halted
Running ‘exporting-methods.R’ [2s/3s]
  Running ‘mahal-dist.R’ [3s/3s]
  Running ‘testthat.R’ [22s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ── 1. Error: Bigglm distances (@test.match_on.R#298)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.match_on.R:298
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ── 2. Error: scores with bigglm (@test.scores.R#222)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.scores.R:222
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1308 SKIPPED: 0 FAILED: 2
  1. Error: Bigglm distances (@test.match_on.R#298) 
  2. Error: scores with bigglm (@test.scores.R#222) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [245s/362s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(peakPantheR)
  
  This is peakPantheR version 1.2.0 
  
  > 
  > test_check("peakPantheR")
  ── 1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180)  ────
  unused arguments (limits, n)
  1: evaluate_promise(annotationDiagnosticMultiplot(input_plots)) at testthat/test_annotationDiagnosticMultiplot.R:180
  2: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  3: force(code)
  4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  5: withVisible(code)
  6: annotationDiagnosticMultiplot(input_plots)
  7: ggplot2::layer_scales(tmp_rtPeakwidthVert)
  8: ggplot_build(plot)
  9: ggplot_build.ggplot(plot)
  10: layout$setup_panel_params()
  ...
  16: f(..., self = self)
  17: parent$setup_panel_params(scale_x, scale_y, params)
  18: f(..., self = self)
  19: train_cartesian(scale_x, self$limits$x, "x")
  20: scale$break_info(range)
  21: f(..., self = self)
  22: ggproto_parent(ScaleContinuous, self)$break_info(range)
  23: f(..., self = self)
  24: self$get_breaks_minor(b = major, limits = range)
  25: f(..., self = self)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  fdouble_metaphone.c:268:5: 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/PGRdup.Rcheck/00install.out’ for details.
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
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.
Running ‘testthat.R’ [32s/83s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ranger)
  > 
  > test_check("ranger")
  ── 1. Failure: maxstat corrected impurity importance is positive (on average) (@
  mean(rf$variable.importance) is not strictly more than 0. Difference: -0.202
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 545 SKIPPED: 9 FAILED: 1
  1. Failure: maxstat corrected impurity importance is positive (on average) (@test_maxstat.R#41) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Wed Mar 13 06:49:41 AM 2019 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
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.
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: 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/RecordLinkage.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:101:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:139:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:131:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘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:
  RngStream.c:347:4: 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/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [9s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  ── 1. Failure: (unknown) (@test_rnn.R#66)  ─────────────────────────────────────
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 995608 - 888626 == 106982
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running ‘testthat.R’ [6s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-translate_sql.R#22)  --------------------------
  translate_sql(as(x, 0), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DOUBLE)").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS DOUBLE)"
  
  -- 2. Failure: as() works (@test-translate_sql.R#26)  --------------------------
  translate_sql(pmax(x), con = s[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-translate_sql.R#30)  --------------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS ARRAY<VARCHAR>)").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS ARRAY<VARCHAR>)"
  
  -- 4. Failure: as() works (@test-translate_sql.R#39)  --------------------------
  translate_sql_(list(substituted.expression), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DATE)").
  1/1 mismatches
  x[1]: "AS(\"x\", '2019-03-13')"
  y[1]: "CAST(\"x\" AS DATE)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 276 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-translate_sql.R#22) 
  2. Failure: as() works (@test-translate_sql.R#26) 
  3. Failure: as() works (@test-translate_sql.R#30) 
  4. Failure: as() works (@test-translate_sql.R#39) 
  
  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/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 significant warnings:
  RngStreams.c:332:4: 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/rstream.Rcheck/00install.out’ for details.
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/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [55s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scdensity)
  > 
  > test_check("scdensity")
  ── 1. Error: all bandwidth options work okay (@testScdensity.R#13)  ────────────
  solve.QP encountered numerical problems and could not find a solution.
  Small changes to the inputs may resolve this.
  1: scdensity(x, bw = "SJ") at testthat/testScdensity.R:13
  2: stop(paste0("solve.QP encountered numerical problems and could not find a solution.\n", 
         "Small changes to the inputs may resolve this."))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 38 SKIPPED: 2 FAILED: 1
  1. Error: all bandwidth options work okay (@testScdensity.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdnet.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.
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.
Running ‘testGBHProcedures.R’ [4s/4s]
  Running ‘testHierarchicalMethods.R’ [3s/4s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
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:
  RngStream.c:347:4: 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/TPmsm.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AbsFilterGSEA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/acc.Rcheck/00install.out' for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ACTCD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/AdaptGauss.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/adaptiveGPCA.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/advclust.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ahnr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AIG.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/alignfigR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/alphahull.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/apsimr.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
Running 'testthat.R' [48s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  -- 1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  dim(df1) not equal to c(4, 16).
  1/2 mismatches
  [1] 5 - 4 == 1
  
  -- 2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$linf[3] not equivalent to 87.4.
  1/1 mismatches
  [1] 75.1 - 87.4 == -12.3
  
  -- 3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$k[2] not equivalent to 0.15.
  1/1 mismatches
  [1] 0.53 - 0.15 == 0.38
  
  -- 4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$locality[1] not equivalent to "Central Adriatic, 100-200 m depth".
  1/1 mismatches
  x[1]: "northeast Mediterranean Sea"
  y[1]: "Central Adriatic, 100-200 m depth"
  
  == testthat results  ===========================================================
  OK: 193 SKIPPED: 1 FAILED: 4
  1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#6) 
  2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#7) 
  3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#8) 
  4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/backShift.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
Packages suggested but not available for checking: 'bcmapsdata' 'doMC'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/bdscale.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/beezdemand.Rcheck/00install.out' for details.
installed size is 152.5Mb
  sub-directories of 1Mb or more:
    include  151.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/billboarder.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/blandr.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
Error in re-building vignettes:
  ...
Quitting from lines 70-80 (BlissIntro.Rmd) 
Error: processing vignette 'BlissIntro.Rmd' failed with diagnostics:
Mat::operator(): index out of bounds
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/blorr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/breakDown.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/brt.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/camtrapR.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ClinReport.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Compind.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/DataPackageR.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/difNLR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Directional.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/DirichletReg.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.1Mb
    libs   2.0Mb
Error in re-building vignettes:
  ...
Loading dodgr
Re-compiling dodgr
Loading dodgr
Quitting from lines 38-38 (dodgr.Rmd) 
Error: processing vignette 'dodgr.Rmd' failed with diagnostics:
'arg' should be one of "pdflatex", "xelatex", "lualatex"
Execution halted
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "doMPI.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'doMPI'. The following files exist in directory '.': 'Rplots.pdf', 'doMPI-012.pdf', 'doMPI.Rnw', 'doMPI.tex'
Calls: buildVignettes -> find_vignette_product
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    appinformation   9.6Mb
    media            1.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.6Mb
    libs   5.0Mb
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: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/emojifont.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/feature.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'gWidgets' 'tcltk' 'tkrplot' 'RGtk2' 'gWidgetsRGtk2' 'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking: 'doMC' 'RSvgDevice'
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Running examples in 'genBaRcode-Ex.R' failed
The error most likely occurred in:

> ### Name: plotClusterGgTree
> ### Title: Plotting a Cluster ggTree
> ### Aliases: plotClusterGgTree
> 
> ### ** Examples
> 
> data(BC_dat)
> plotClusterGgTree(BC_dat, tree_est = "UPGMA", type = "circular")
Error: object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/gfcanalysis.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggcorrplot.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggfittext.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggplot2.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggplotify.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gifti)
  > 
  > test_check("gifti")
  trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  -- 1. Error: reading gifti files (@test-reader.R#3)  ---------------------------
  cannot open URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  1: download_gifti_data(tdir) at testthat/test-reader.R:3
  2: download.file(url = url, destfile = destfile)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: reading gifti files (@test-reader.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
Quitting from lines 43-46 (Reading_GIFTI_Files.Rmd) 
Error: processing vignette 'Reading_GIFTI_Files.Rmd' failed with diagnostics:
cannot open URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Error in re-building vignettes:
  ...
pandoc.exe: Could not fetch https://codecov.io/gh/MarkEdmondson1234/googleAuthR/branch/master/graph/badge.svg
HttpExceptionRequest Request {
  host                 = "codecov.io"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/gh/MarkEdmondson1234/googleAuthR/branch/master/graph/badge.svg"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 NoResponseDataReceived
Error: processing vignette 'advanced-building.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/GPareto.Rcheck/00install.out' for details.
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/3.6/gpuR.Rcheck/00install.out' for details.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
Packages suggested but not available for checking:
  'taxstats' 'taxstats1516'
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 88.77014
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 47.40032
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 84.1606
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 36.74531
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Error in re-building vignettes:
  ...
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-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-35\unhbox\voidb@x \penalty \@M \ {}1.
3/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Hapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/harrietr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/hergm.Rcheck/00install.out' for details.
Error in .requirePackage(package) : 
    unable to find required package 'HiTC'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/HighDimOut.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/HLMdiag.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   2.9Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Depends: includes the non-default packages:
  'lattice' 'caTools' 'gdata' 'gtools' 'gplots' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/IncDTW.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Information.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/InformationValue.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'gurobi' 'Rcplex' 'cplexAPI'
Found the following significant warnings:
  Warning: S3 methods '.DollarNames.Message', '.DollarNames.Descriptor', '.DollarNames.EnumDescriptor', '.DollarNames.EnumValueDescriptor', '.DollarNames.FileDescriptor', '.DollarNames.FieldDescriptor', '.DollarNames.ServiceDescriptor', '.DollarNames.MethodDescriptor', '.DollarNames.ZeroCopyInputStream', '.DollarNames.ZeroCopyOutputStream', 'with.Message', 'within.Message', 'as.list.Message', 'as.list.Descriptor', 'as.list.EnumDescriptor', 'as.list.FileDescriptor', 'as.list.ServiceDescriptor' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/jmvcore.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...

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 327-331 (awesome_table_in_html.Rmd) 
Error: processing vignette 'awesome_table_in_html.Rmd' failed with diagnostics:
unused arguments ("Group 1", 4, 7)
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Packages suggested but not available for checking:
  'koRpus.lang.de' 'koRpus.lang.es' 'koRpus.lang.fr' 'koRpus.lang.it'
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/LBSPR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/LexisPlotR.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Depends: includes the non-default packages:
  'sn' 'moments' 'BB' 'Bolstad2' 'optimx' 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.2Mb
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/mDAG.Rcheck/00install.out' for details.
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.
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
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.
INFORMATION: Es konnten keine Dateien mit dem angegebenen
Muster gefunden werden.
Quitting from lines 63-72 (metaBMA.Rmd) 
Error: processing vignette 'metaBMA.Rmd' failed with diagnostics:
Unable to call JAGS
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MetaLonDA.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'doMC' 'doSMP'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/metR.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.1Mb
    misc   1.1Mb
Unknown package 'microcontax.data' in Rd xrefs
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MKmisc.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/mlr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MortalityTables.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MSCMT.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'amap' 'clValid' 'cluster' 'fpc' 'mzR' 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.5/msgps.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'car' 'pdist' 'pls' 'gplots' 'mvtnorm' 'robustbase' 'gtools' 'bitops'
  'caTools' 'pcaPP' 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running 'testthat.R' [69s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  -- 1. Failure: covex-E (@test_covex.R#54)  -------------------------------------
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.913 - 0.947 == -0.0334
  0.5
  
  -- 2. Failure: covex-E (@test_covex.R#54)  -------------------------------------
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.827 - 0.947 == -0.12
  0.9
  
  -- 3. Failure: covex-E (@test_covex.R#54)  -------------------------------------
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.825 - 0.947 == -0.122
  1
  
  == testthat results  ===========================================================
  OK: 172 SKIPPED: 2 FAILED: 3
  1. Failure: covex-E (@test_covex.R#54) 
  2. Failure: covex-E (@test_covex.R#54) 
  3. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NBLDA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NeatMap.Rcheck/00install.out' for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.7Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.5Mb
Running 'test-all.R' [11s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > if(require("testthat", quietly = TRUE)) {
  +     test_check("nloptr")
  + } else {
  +     print( "package 'testthat' not available, cannot run unit tests" )
  + }
  Loading required package: nloptr
  -- 1. Failure: Test that solver stops when maxtime is reached. (@test-options-ma
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 1 - 6 == -5
  
  == testthat results  ===========================================================
  OK: 46 SKIPPED: 0 FAILED: 1
  1. Failure: Test that solver stops when maxtime is reached. (@test-options-maxtime.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NMF.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'lpSolve' 'gdata' 'Hmisc' 'rms' 'geometry' 'psych' 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NutrienTrackeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/obliqueRSF.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
Running examples in 'OData-Ex.R' failed
The error most likely occurred in:

> ### Name: entitySets
> ### Title: Get a list of EntitySets for a web service base on OData
> ### Aliases: entitySets
> 
> ### ** Examples
> 
> entitySets("http://services.odata.org/TripPinRESTierService/?$format=json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: entitySets -> <Anonymous> -> paste -> readLines -> file
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/OmicsPLS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/OpasnetUtils.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     6.7Mb
    models   4.7Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/overlapping.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PCADSC.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PCMBase.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PDN.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PedCNV.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PGRdup.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PhaseType.Rcheck/00install.out' for details.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") : 
  cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw-midday.txt'
Warning in get_midday_list(site, direct = FALSE) :
  download from the phenocam server was failed
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  Loading required package: bitops
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Error in download.file(url, destfile = tmp, mode = "w") : 
    cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  -- 1. Error: (unknown) (@testphenocamapi.R#11)  --------------------------------
  file was not found on the server!
  1: get_pheno_ts(site = "dukehw", vegType = "DB", roiID = 1000, type = "3day") at testthat/testphenocamapi.R:11
  2: stop("file was not found on the server!")
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testphenocamapi.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Quitting from lines 200-209 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
file was not found on the server!
Execution halted
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PKgraph.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/plotROC.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/POUMM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PPtreeViz.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PReMiuM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PRISMA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ProgGUIinR.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  > options(testthat.use_colours = FALSE)
  > test_check("psd")
  Loading required package: psd
  Loaded psd (1.0.1) -- Adaptive multitaper spectrum estimation
  -- 1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26)  ----------
  `FFT(x.)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 161 SKIPPED: 0 FAILED: 1
  1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
-----------------------------------------------------  psychmeta version 2.3.2  --

Please report any bugs to github.com/psychmeta/psychmeta/issues
or issues@psychmeta.com

We work hard to produce these open-source tools for the R community, 
please cite psychmeta when you use it in your research: 
  Dahlke, J. A., & Wiernik, B. M. (2018). psychmeta: An R package for 
     psychometric meta-analysis. Applied Psychological Measurement. 
     Advance online publication. https://doi.org/10.1177/0146621618795933

Find info about psychmeta on the web at psychmeta.com and twitter.com/psychmetaR
Error: package or namespace load failed for 'psychmeta':
 .onAttach failed in attachNamespace() for 'psychmeta', details:
  call: open.connection(x, "rb")
  error: cannot open the connection
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.5Mb
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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/QuantumClone.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/quickPlot.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/RaceID.Rcheck/00install.out' for details.
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/randstr.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RATest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/raustats.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.7Mb
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Rcmdr.Rcheck/00install.out' for details.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: (unknown) (@test_deputados.R#81)  ---------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  -- 2. Error: (unknown) (@test_proposicoes.R#91)  -------------------------------
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  -- 3. Error: (unknown) (@test_votacoes.R#70)  ----------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

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 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
Running examples in 'rcv-Ex.R' failed
The error most likely occurred in:

> ### Name: import_data
> ### Title: Imports election data
> ### Aliases: import_data
> 
> ### ** Examples
> 
> import_data("http://www.sfelections.org/results/20161108/data/20161206/20161206_masterlookup.txt",
+  header = FALSE)
`curl` package not installed, falling back to using `url()`
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: import_data ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'
No data available for station MY1
Warning: Unknown or uninitialised column: 'unit'.
Warning: Unknown or uninitialised column: 'unit'.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning: Unknown or uninitialised column: 'datetime'.
Quitting from lines 117-123 (rdefra_vignette.Rmd) 
Error: processing vignette 'rdefra_vignette.Rmd' failed with diagnostics:
do not know how to convert 'df$datetime' to class "POSIXlt"
Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdhs)
  > 
  > Sys.setenv("rdhs_RENVIRON_PERMISSION" = 1)
  > test_check("rdhs")
  -- 1. Error: update_rdhs_config (@test_miscellaneous.R#97)  --------------------
  cannot open the connection
  1: dhs_data_updates() at testthat/test_miscellaneous.R:97
  2: handle_api_request(endpoint, query, all_results, client, force)
  3: check_for_client()
  4: rdhs_setup()
  5: client_dhs(config = config, root = config$cache_path)
  6: R6_client_dhs$new(config, api_key, root)
  7: .subset2(public_bind_env, "initialize")(...)
  8: saveRDS(self, file.path(root, client_file_name()))
  9: gzfile(file, mode)
  
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZMR61FL.ZIP&Tp=1&Ctry_Code=zz&survey_id=0&doctype=dhs'
  Content type 'application/x-zip-compressed' length 597481 bytes (583 KB)
  ==================================================
  downloaded 583 KB
  
    adding: temp/RtmpkF45dK/file15294310b155b/ZZMR61FL.DAT (deflated 85%)
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZAR61FL.ZIP&Tp=4&Ctry_Code=zz&survey_id=0&doctype=hiv'
  Content type 'application/x-zip-compressed' length 81939 bytes (80 KB)
  ==================================================
  downloaded 80 KB
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 42 FAILED: 1
  1. Error: update_rdhs_config (@test_miscellaneous.R#97) 
  
  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/3.5/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rfishbase.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/rgbif.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RGraphics.Rcheck/00install.out' for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
Error in re-building vignettes:
  ...
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'

Quitting from lines 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RIdeogram.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in 'RISmed-Ex.R' failed
The error most likely occurred in:

> ### Name: Cited
> ### Title: Number of citations
> ### Aliases: Cited
> 
> ### ** Examples
> 
> res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
> Cited(res)
Warning in readLines(the_url) :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Too Many Requests'
Error in readLines(the_url) : cannot open the connection
Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
Execution halted
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/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/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Rmagic.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rmytarget.Rcheck/00install.out' for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R  11.0Mb
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
S3 methods shown with full name in documentation object 'cbind.fill':
  'cbind.fill'

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:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RSA.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...

Error: processing vignette 'rscala.Rnw' failed with diagnostics:
 chunk 7 (label = Instantiate a bridge for this document) 
Error in scalaConnect(details) : missing value where TRUE/FALSE needed
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/3.5/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/3.5/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/3.5/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.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
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) (2017-12-30 r73992)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) 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_3.5.0
> 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 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/SCRABBLE.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R   7.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/sensobol.Rcheck/00install.out' for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
Error in re-building vignettes:
  ...
trying URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
Quitting from lines 38-41 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/SHT.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'hdrcde' 'coda' 'MASS' 'bayesm' 'mnormt' 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/SimMultiCorrData.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SiMRiv)
  Loading required package: raster
  Loading required package: sp
  
  Attaching package: 'SiMRiv'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("SiMRiv")
  -- 1. Failure: Random walk is not biased (@test-simulations.R#35)  -------------
  chisq.test(headings)$p.value is not strictly more than 0.01. Difference: -0.0069
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Failure: Random walk is not biased (@test-simulations.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [192s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
    Using cached copy of .inputObjects event in test module.   
  -- 1. Failure: simulation runs with simInit and spades (@test-simulation.R#86)  
  mySim$caribou$x not equivalent to `pos_x`.
  100/100 mismatches (average diff: 9.83)
  [1]   3.67 -   1.06 ==   2.613
  [2]  43.57 -  44.45 ==  -0.883
  [3]  47.23 -  45.88 ==   1.351
  [4]   3.60 -  -1.32 ==   4.918
  [5]  20.23 -  17.86 ==   2.370
  [6] -47.81 -  48.48 == -96.294
  [7]  16.55 -  10.75 ==   5.796
  [8] -21.41 - -24.63 ==   3.218
  [9] -47.28 - -48.51 ==   1.234
  ...
  
  -- 2. Failure: simulation runs with simInit and spades (@test-simulation.R#87)  
  mySim$caribou$y not equivalent to `pos_y`.
  100/100 mismatches (average diff: 5.15)
  [1] -15.00 - -15.90 ==  0.898
  [2]  -5.35 -  -8.97 ==  3.616
  [3]  19.51 -  25.27 == -5.758
  [4] -36.40 - -39.07 ==  2.674
  [5] -33.64 - -32.96 == -0.678
  [6]  15.57 -  19.59 == -4.027
  [7]  15.12 -  14.87 ==  0.249
  [8]  39.63 -  38.26 ==  1.368
  [9]  -6.33 -  -8.17 ==  1.831
  ...
  
    Using cached copy of .inputObjects event in child6 module.   
    Using memoised copy of .inputObjects event in child6 module
    Using memoised copy of .inputObjects event in child6 module
  == testthat results  ===========================================================
  OK: 457 SKIPPED: 32 FAILED: 2
  1. Failure: simulation runs with simInit and spades (@test-simulation.R#86) 
  2. Failure: simulation runs with simInit and spades (@test-simulation.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/SparseFactorAnalysis.Rcheck/00install.out' for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.0Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/speaq.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/spotifyr.Rcheck/00install.out' for details.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(statsDK)
  > 
  > test_check("statsDK")
  -- 1. Failure: we have indeed received data (@test_retrievers.R#47)  -----------
  is.data.frame(pris) isn't true.
  
  -- 2. Failure: we have indeed received data (@test_retrievers.R#48)  -----------
  nrow(pris) > 0 isn't true.
  
  -- 3. Failure: we have indeed received data (@test_retrievers.R#49)  -----------
  ncol(pris) > 0 isn't true.
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 3
  1. Failure: we have indeed received data (@test_retrievers.R#47) 
  2. Failure: we have indeed received data (@test_retrievers.R#48) 
  3. Failure: we have indeed received data (@test_retrievers.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/StempCens.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/STMotif.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("http://goo.gl/VPdxlS")) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/SubgrpID.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/survMisc.Rcheck/00install.out' for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  -- 1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  cannot open URL 'http://www.europarl.europa.eu/oeil/popups/printfichetechnical.pdf?id=673511&lang=fr'
  1: extract_text(f2, page = 1, encoding = "latin1") at testthat/test_non-latin.R:15
  2: load_doc(file, password = password, copy = copy)
  3: localize_file(path = file, copy = copy)
  4: utils::download.file(path, tmp, quiet = quiet, mode = "wb")
  
  == testthat results  ===========================================================
  OK: 90 SKIPPED: 0 FAILED: 1
  1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TDAstats.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TippingPoint.Rcheck/00install.out' for details.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TOSTER.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TPD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TPMplt.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/treemap.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TSCS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TSMining.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/UpSetR.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'vaers' 'vaersND'
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: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/vegan3d.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    doc    1.2Mb
    help   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/WeMix.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 23-26 (Running_WhiteStripe.Rmd) 
Error: processing vignette 'Running_WhiteStripe.Rmd' failed with diagnostics:
cannot open URL 'http://muschellij2.github.io/WhiteStripe/T1Strip.nii.gz'
Execution halted
Error in re-building vignettes:
  ...

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 78-81 (wikisourcer.Rmd) 
Error: processing vignette 'wikisourcer.Rmd' failed with diagnostics:
HTTP error 404.
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/WVPlots.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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:
  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/3.5/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    6.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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/3.5/adamethods.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
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: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/adiv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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/3.5/AFM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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
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/3.5/AIG.Rcheck/00install.out’ for details.
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.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
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 21.3Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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
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/3.5/Anthropometry.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
Error: processing vignette 'help.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
installed size is 93.5Mb
  sub-directories of 1Mb or more:
    libs  93.0Mb
Package suggested but not available for checking: ‘testthat’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...

Returned 'NA'!


No TSN found for species 'Juniperus occidentalis'!


Retrieving data for taxon 'Pinus strobus'





More than one TSN found for taxon 'Pinus strobus'!

            Enter rownumber of taxon (other inputs will return 'NA'):


Returned 'NA'!


No TSN found for species 'Pinus strobus'!


Execution halted
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/3.5/aqr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TDA’
Error in re-building vignettes:
  ...
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
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.1Mb
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/3.5/Arothron.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [24s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 338 SKIPPED: 0 FAILED: 26
  1. Failure: write2.tableby -> HTML (@test_write2.R#28) 
  2. Failure: write2.tableby -> HTML (@test_write2.R#28) 
  3. Failure: write2.modelsum -> HTML (@test_write2.R#34) 
  4. Failure: write2.modelsum -> HTML (@test_write2.R#34) 
  5. Failure: write2.freqlist -> HTML (@test_write2.R#42) 
  6. Failure: write2.freqlist -> HTML (@test_write2.R#42) 
  7. Failure: write2.freqlist -> doc (@test_write2.R#47) 
  8. Failure: write2.freqlist -> doc (@test_write2.R#47) 
  9. Failure: write2.list (summary objects) -> PDF (@test_write2.R#59) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ 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/3.5/audio.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘fgsea’ ‘ConsensusClusterPlus’ ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.5Mb
Package suggested but not available for checking: ‘philr’
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   2.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...
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.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

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/3.5/BAT.Rcheck/00install.out’ for details.
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/3.5/bayesCL.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.7Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  15.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.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  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.1Mb
Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 61.6Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
Error in re-building vignettes:
  ...
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
Execution halted
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 149.6Mb
  sub-directories of 1Mb or more:
    include  149.6Mb
Running ‘testthat.R’ [1s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10009 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.8Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot1782b14a0857a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1782b14a0857a.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.9Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$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 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘mzR’

Package suggested but not available for checking: ‘metaboData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’ ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bioacoustics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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
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/3.5/Biocomb.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocStyle’
Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (IntroBiofiles.Rnw) 
Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Packages required but not available: ‘ChemmineR’ ‘fmcsR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Error in re-building vignettes:
  ...
 For citation see: citation("bipartite").
 Have a nice time plotting and analysing two-mode networks.


Attaching package: 'bipartite'

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

    nullmodel


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 42-54 (bipartiteD3_Intro.Rmd) 
Error: processing vignette 'bipartiteD3_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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 required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.3Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: ‘sangerseqR’
Package unavailable to check Rd xrefs: ‘rosr’
installed size is 328.9Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      325.6Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
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/3.5/bpca.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RGtk2’ ‘cairoDevice’
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 34.2Mb
  sub-directories of 1Mb or more:
    libs  34.0Mb
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$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 120, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = "m")$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
Package suggested but not available for checking: ‘pasilla’
Packages required but not available: ‘DiffBind’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BSquare.Rcheck/00install.out’ for details.
installed size is 25.2Mb
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    libs  24.2Mb
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs  79.0Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Error in re-building vignettes:
  ...

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]="./webshotb3c71d491160.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb3c71d491160.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
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cairoDevice.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.3-6, (SVN revision 773)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.3-1 
Warning in engine$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 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
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 `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
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:
duplicate rownames not allowed
Execution halted
Package required but not available: ‘OpenCL’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
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    doc    3.5Mb
    libs   3.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error in re-building vignettes:
  ...
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

     Hanna Meyer, Christoph Reudenbach, Marvin Ludwig, Thomas Nauss
     _Maintainer:_ Hanna Meyer <email: hanna.meyer@geo.uni-marburg.de>


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]="./webshot2c6d78301f9d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2c6d78301f9d.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.8Mb
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    libs   5.1Mb
installed size is  5.4Mb
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    data      1.2Mb
    extdata   1.1Mb
    libs      2.8Mb
installed size is 14.8Mb
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    libs  14.5Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CCMnet.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
installed size is  9.5Mb
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    extdata   9.2Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.5Mb
Running ‘test_changepoints.R’ [1s/1s]
Running the tests in ‘tests/test_changepoints.R’ failed.
Last 13 lines of output:
  [1] 88 10
  [1] 12 10
  [1] 89 10
  [1] 11 10
  [1] 90 10
  [1] 10 10
  [1] 77 10
  [1] 23 10
  > stopifnot(changepoints_mod@changepoints == 77)
  > 
  > # test rank one
  > res_ro = rank_one(scp_data, init, update_w=0.1, regularizer=0.1)
  > stopifnot(res_ro$tau == 56)
  Error: res_ro$tau == 56 is not TRUE
  Execution halted
Packages suggested but not available for checking:
  ‘GenomicInteractions’ ‘Gviz’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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'
Execution halted
Error in re-building vignettes:
  ...
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 42-44 (access_childes_db.Rmd) 
Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
Execution halted
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FRAPO’
Package unavailable to check Rd xrefs: ‘FRAPO’
installed size is  6.3Mb
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    libs   6.2Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clpAPI.Rcheck/00install.out’ for details.
Packages required but not available: ‘rggobi’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [10s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("clustree")
  ── 1. Error: show_axis works (@test-clustree.R#79)  ────────────────────────────
  object 'sce' not found
  1: expect_is(clustree(sce, prefix = "sc3_", suffix = "_clusters", show_axis = TRUE), 
         c("gg", "ggplot")) at testthat/test-clustree.R:79
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sce, prefix = "sc3_", suffix = "_clusters", show_axis = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 49 SKIPPED: 4 FAILED: 1
  1. Error: show_axis works (@test-clustree.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  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!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘InteractionSet’ ‘GenomicFeatures’ ‘GenomicInteractions’
  ‘rtracklayer’ ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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.

LABELLED 2.0.0: BREAKING CHANGE

Following version 2.0.0 of `haven`, `labelled()` and `labelled_spss()` now produce objects with class 'haven_labelled' and 'haven_labelled_spss', due to conflict between the previous 'labelled' class and the 'labelled' class used by `Hmisc`.

A new function `update_labelled()` could be used to convert data imported with an older version of `haven`/`labelled` to the new classes.

Quitting from lines NA-15 (codebook.Rmd) 
Error: processing vignette 'codebook.Rmd' failed with diagnostics:
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Execution halted
installed size is  5.0Mb
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    doc       2.2Mb
    extdata   2.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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/3.5/colourvision.Rcheck/00install.out’ for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.2Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompRandFld.Rcheck/00install.out’ for details.
installed size is 47.5Mb
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    libs  46.4Mb
Error in re-building vignettes:
  ...
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 131-143 (Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd) 
Error: processing vignette 'Tutorial_Cleaning_GBIF_data_with_CoordinateCleaner.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  9.3Mb
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    R     2.1Mb
    doc   5.0Mb
Package suggested but not available for checking: ‘ProData’
installed size is 18.3Mb
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    libs  17.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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installed size is 37.7Mb
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    libs  37.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cplexAPI.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
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 84-86 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Program 'git' terminated (timeout reached: 10.00sec)
Execution halted
Package suggested but not available for checking: ‘clusterProfiler’
Error in re-building vignettes:
  ...
    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim


Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/crplyr.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 21.9Mb
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    libs  20.2Mb
installed size is 88.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  84.2Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 142-152 (truncated_tesseract.Rmd) 
Error: processing vignette 'truncated_tesseract.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
The following objects are masked from 'package:stats':

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'cowplot'

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

    ggsave

Loading required package: boot
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
Loading required package: magrittr
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 110-166 (robust-statistical-visualization.Rmd) 
Error: processing vignette 'robust-statistical-visualization.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Packages required but not available: ‘RGtk2’ ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
Running ‘testthat.R’ [24s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         message <- DataPackageError$new(stringr::str_interp("Not resolved Remote URI \"${value}\" for descriptor[[${property}]]"))$message
         stop(message)
     })
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  12: stop(message)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 245 SKIPPED: 0 FAILED: 2
  1. Error: remote (@test-package.R#226) 
  2. Error: remote (@test-resource.R#163) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  55.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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]="./webshot2dd96169dbd5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2dd96169dbd5.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing or unexported object: ‘dplyr::group_rows’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.4Mb
Error in re-building vignettes:
  ...
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: package 'dplyr' was built under R version 3.5.1

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:
cannot open the connection
Execution halted
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  58.1Mb
Error in re-building vignettes:
  ...

    cutree

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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: 'gplots'

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

    bluered, greenred

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

    lowess

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 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.6Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Running ‘test-that.R’ [88s/93s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
  Loading required package: devtools
  Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  ── 1. Error: Package readme can be built  (@test-build-readme.R#8)  ────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: build_readme("testReadme") at testthat/test-build-readme.R:8
  2: callr::r(build, args = list(pkg_path = pkg$path, readme_path = readme_path, ... = ..., 
         quiet = quiet), show = TRUE, spinner = FALSE)
  3: get_result(output = out, options)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 11 FAILED: 1
  1. Error: Package readme can be built  (@test-build-readme.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  50.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.6Mb
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("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Package suggested but not available for checking: ‘pcaL1’
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> ### Name: PCA_L1-class
> ### Title: Principal Component Analysis with L1 error.
> ### Aliases: PCA_L1-class PCA_L1
> 
> ### ** Examples
> 
> dat <- loadDataSet("Iris")
> 
> ## using the S4 Class
> pca_l1 <- PCA_L1()
> emb <- pca_l1@fun(dat, pca_l1@stdpars)
Error in chckpkg("pcaL1") : 
  require 'pcaL1' package, install it using install.packages('pcaL1')
Calls: <Anonymous> -> chckpkg
Execution halted
Running ‘testthat.R’ [110s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'dimRed'
  
  The following object is masked from 'package:stats':
  
      embed
  
  The following object is masked from 'package:base':
  
      as.data.frame
  
  > 
  > test_check("dimRed", reporter = ListReporter)
  Error: Test failures
  Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Package which this enhances but not available for checking: ‘RobExtremes’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.1Mb
    libs   3.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   6.4Mb
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.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:
    libs   5.2Mb
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: 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/3.5/DPWeibull.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot82df58bae368.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot82df58bae368.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.3Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.6Mb
    libs  20.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 62.7Mb
  sub-directories of 1Mb or more:
    libs  62.1Mb
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/emIRT.Rcheck/00install.out’ for details.
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> cinp.daily.dir  <- system.file("shiny/EmiStatR_inputCSO/inputCSO", package = "EmiStatR")
> cinp.daily.file <- paste(cinp.daily.dir, "/qs_factor.csv", sep="")
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> 
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Running ‘testthat.R’ [82s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  18: as(set_TextType(methods_file), "description")
  19: .class1(object)
  20: set_TextType(methods_file)
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 78 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Packages required but not available: ‘xcms’ ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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:
cannot open the connection
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiStats.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Running examples in ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> ### Name: LModularity
> ### Title: L Modularity
> ### Aliases: LModularity
> 
> ### ** Examples
> 
> # A modular matrix:
> modules = matrix(c(rep(c(1, 0, 0), each = 5),
+ rep(c(0, 1, 0), each = 5),
+ rep(c(0, 0, 1), each = 5)), 15)
> cor.hypot = CreateHypotMatrix(modules)[[4]]
> hypot.mask = matrix(as.logical(cor.hypot), 15, 15)
> mod.cor = matrix(NA, 15, 15)
> mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
> mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
> diag(mod.cor) = 1
> mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric
> 
> LModularity(mod.cor)
Error in method(g, ...) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Calls: LModularity -> method
Execution halted
Running ‘testthat.R’ [173s/275s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: plyr
  ── 1. Error: LModularity resturn resonable results (@test.LModularity.r#12)  ───
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: expect_equal(modules, LModularity(mod.cor)[[2]]) at testthat/test.LModularity.r:12
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: LModularity(mod.cor)
  5: method(g, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20953 SKIPPED: 1 FAILED: 1
  1. Error: LModularity resturn resonable results (@test.LModularity.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘exampletestr-Ex.R’ failed
The error most likely occurred in:

> ### Name: make-test-shells
> ### Title: Create test shells.
> ### Aliases: make-test-shells make_test_shell_fun make_tests_shells_file
> ###   make_tests_shells_pkg
> 
> ### ** Examples
> 
> usethis::create_package(tempdir(check = TRUE), open = FALSE)
Error: '/tmp' is not a directory.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: withVisible(eval(expr, pf))
  7: eval(expr, pf)
  8: eval(expr, pf)
  9: usethis::create_package(tempdir(), open = FALSE)
  10: create_directory(path_dir(path), name)
  11: stop_glue("{value(base_path)} is not a directory.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: `extract_examples()` works (@test-exemplar.R#7) 
  2. Error: `make_test_shell()` works (@test-exemplar.R#47) 
  3. Error: `make_tests_shell_fun()` works (@test-exemplar.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    exiftool  13.0Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fastR2.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Found the following significant warnings:
  Rconnection.cc:347:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  Rconnection.cc:356:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.5Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Running ‘test-as-dgCMatrix.R’ [3s/4s]
  Running ‘test-empty_array.R’ [3s/4s]
  Running ‘test-existence_collision.R’ [2s/4s]
  Running ‘test-hash.mapping.R’ [2s/4s]
  Running ‘test-hashing.R’ [3s/4s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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/3.5/fingerPro.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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: Removed 2 rows containing missing values (geom_point).
Warning in normalizePath(f2) :
  path[1]="./webshotbdf6a0122b7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotbdf6a0122b7.png': No such file or directory
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
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 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.4Mb
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Package suggested but not available for checking: ‘devEMF’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   4.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  55.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
Package suggested but not available for checking: ‘RTCGA.rnaseq’
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘doMPI’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.6Mb
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  71.8Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     49.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.9Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gdmp.Rcheck/00install.out’ for details.
Package required but not available: ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
S3 methods shown with full name in documentation object 'diseq':
  ‘diseq.ci’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'User_manual.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `USenglish'. Either you misspelled it
(babel)                or the language definition file USenglish.ldf was not fo
und.

See the babel package documentation for explanation.
! Package babel Error: You haven't specified a language option.

See the babel package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
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/3.5/geoelectrics.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   3.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R         5.7Mb
    extdata   1.3Mb
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/3.5/geomorph.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
Error in setClass("Extent", representation(xmin = "numeric", xmax = "numeric",  : 
  could not find function "setClass"
Package suggested but not available for checking: ‘RGtk2’
Error in re-building vignettes:
  ...
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 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GFORCE.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  18.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ggraptR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x123629579
#1  0x123628945
#2  0x7fff93ac4529
sh: line 1: 96924 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/RtmpLCaVyQ/x1317a8c540f25fd/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1235f6579
#1  0x1235f5945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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 (msgimme-vignette.Rmd) 
Error: processing vignette 'msgimme-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  58.5Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
cannot open the connection
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/3.5/GPoM.Rcheck/00install.out’ for details.
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Packages required but not available:
  ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
  ‘EnsDb.Mmusculus.v79’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘GenomicFeatures’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
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.
sh: line 1: 29372 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpjUDYzi/x13717e8f67458/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x121f26579
#1  0x121f25945
#2  0x7fff93ac4529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Package which this enhances but not available for checking: ‘RGtk2Extras’

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/3.5/h5.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 95-107 (retype.Rmd) 
Error: processing vignette 'retype.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 335-344 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  HARDataCreationC.cpp:19:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HARModel.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.15.2

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 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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

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/3.5/HierO.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use

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 52-53 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘FKF’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.1Mb
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/3.5/HMMmlselect.Rcheck/00install.out’ for details.
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘MenuCollection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RGtk2’ ‘cairoDevice’ ‘RGtk2Extras’
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.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.
Package suggested but not available for checking: ‘HTSFilter’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   4.5Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
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/3.5/hypervolume.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.6Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IBDsim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘Rglpk’
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   9.0Mb
Package required but not available: ‘graphite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘mixAK’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 55.6Mb
  sub-directories of 1Mb or more:
    libs  54.6Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.0Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     17.1Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: 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/3.5/Immigrate.Rcheck/00install.out’ for details.
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpXpzF0q/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                AminusB               CminusD AminusB.minus.CminusD 
             0.04765402           -0.04765402            0.09530804 
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.03198493            0.03198493            0.12793972 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#26) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
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)
sh: line 1: 29920 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x123592579
#1  0x123591945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

     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:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/jomo.Rcheck/00install.out’ for details.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kerasformula.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmcudaR.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LambertW.Rcheck/00install.out’ for details.
installed size is 79.6Mb
  sub-directories of 1Mb or more:
    libs  78.2Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rtracklayer’
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.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   1.7Mb
    libs      3.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
Package required but not available: ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.2Mb
    testdata   1.6Mb
Error in re-building vignettes:
  ...
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/lmr/m/n/10.95 3
[3]

Package amsmath Warning: Foreign command \atop;
(amsmath)                \frac or \genfrac should be used instead
(amsmath)                 on input line 370.

! Undefined control sequence.
\c@lor@to@ps ->\PSTricks 
                         _Not_Configured_For_This_Format
l.370   \end
            {center}
? 
! Emergency stop.
\c@lor@to@ps ->\PSTricks 
                         _Not_Configured_For_This_Format
l.370   \end
            {center}
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on lmSubsets.log.
make: *** [all] Error 1
Error in buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/lmSubsets.Rcheck/vign_test/lmSubsets") : 
  running 'make' failed
Execution halted
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Package suggested but not available for checking: ‘RDRToolbox’
Error in re-building vignettes:
  ...
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 2-13 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-13 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'loo2-example.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Running ‘testthat.R’ [10s/91s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 147 SKIPPED: 0 FAILED: 2
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#27) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘ggplot2’ ‘knitr’
  All declared Imports should be used.
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  43.5Mb
Error in re-building vignettes:
  ...
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 62-63 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.9Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  14.1Mb
Error in re-building vignettes:
  ...
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

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]="./webshot1b95497e3633.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1b95497e3633.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd023306255d6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd023306255d6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs         14.8Mb
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   7.5Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.1Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

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

Execution halted

... incomplete output.  Crash?
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
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/3.5/MDSMap.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Error in re-building vignettes:
  ...
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: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Loading required package: kinship2
Loading required package: quadprog
Loading required package: gdsfmt
Quitting from lines 694-696 (mega2rtutorial.Rmd) 
Error: processing vignette 'mega2rtutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted
Packages required but not available: ‘RGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.9Mb
Packages suggested but not available for checking: ‘clpAPI’ ‘ctc’
Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...
    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


> library(HTSFilter)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘HTSFilter’
Execution halted
Error in re-building vignettes:
  ...
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance,
    usability and functionality, please consider
    migrating to 'DESeq2'.

Attaching package: ‘DESeq’

The following objects are masked from ‘package:DESeq2’:

    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 9 (label = DESeq1study) 
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
Execution halted
installed size is 43.2Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: 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/3.5/mets.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs  15.8Mb
    misc   1.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error in re-building vignettes:
  ...
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
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
Found the following significant warnings:
  mat.c:1867:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mgcv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘grasp2db’
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.1Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [19s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
Execution halted
File ‘MigClim/libs/MigClim.so’:
  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.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘glpkAPI’
Error in re-building vignettes:
  ...
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
Loading required package: lattice
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'glpkAPI'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.5Mb
Packages suggested but not available for checking: ‘mixAK’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/missDeaths.Rcheck/00install.out’ for details.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Package unavailable to check Rd xrefs: ‘REBayes’
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’
Package required but not available: ‘rsgcc’

Packages suggested but not available for checking:
  ‘GeneSelector’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘minfi’ ‘BiocStyle’ ‘IlluminaHumanMethylation450kmanifest’
Error in re-building vignettes:
  ...
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 27-28 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:variables':

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

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

    geyser

trying URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Warning in download.file("https://zenodo.org/record/17179/files/DVC.tgz",  :
  cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz': HTTP status was '404 Not Found'
Quitting from lines 27-80 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/MM2Sdata.Rnw’
(Is a VignetteBuilder field missing?)
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
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  6.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.0Mb
Running examples in ‘mongolite-Ex.R’ failed
The error most likely occurred in:

> ### Name: gridfs
> ### Title: GridFS API
> ### Aliases: gridfs
> 
> ### ** Examples
> 
> # New GridFS
> fs <- gridfs(url = "mongodb+srv://readwrite:test@cluster0-84vdt.mongodb.net/test")
Error: No suitable servers found (`serverSelectionTryOnce` set): [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-01-84vdt.mongodb.net:27017'] [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate verify failed calling ismaster on 'cluster0-shard-00-02-84vdt.mongodb.net:27017'] [TLS handshake failed: error:1416F086:SSL routines:tls_process_server_certificate:certificate
Execution halted
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
File ‘MRwarping/libs/MRwarping.so’:
  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.
Error in re-building vignettes:
  ...
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.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘mzR’ ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/msigdbr.Rcheck/00install.out’ for details.
Running examples in ‘mssqlR-Ex.R’ failed
Running ‘test-all.R’ [31s/31s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  1: rmarkdown::render(tf, quiet = TRUE) at testthat/test_mudata.io.R:554
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 967 SKIPPED: 0 FAILED: 1
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 84.2Mb
  sub-directories of 1Mb or more:
    libs  84.0Mb
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x10bd4db40, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  28: test_code(NULL, exprs, env)
  29: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  30: force(code)
  31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  32: FUN(X[[i]], ...)
  33: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  34: force(code)
  35: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  36: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  37: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  38: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  39: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
Error in re-building vignettes:
  ...
Warning in engine$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: geometry
Loading required package: magic
Loading required package: abind
Loading required package: rootSolve
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 252-268 (munsellinterpol-guide.Rmd) 
Error: processing vignette 'munsellinterpol-guide.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(temp_file_path) at testthat/test-unname_all_chunks.R:22
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests 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/3.5/nat.templatebrains.Rcheck/00install.out’ for details.
Warning: declared S3 method 'plot3d.templatebrain' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
File ‘NeatMap/libs/NeatMap.so’:
  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.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.6Mb
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.7Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.5Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘noteMD-Ex.R’ failed
The error most likely occurred in:

> ### Name: note_in_html
> ### Title: Print text input in html
> ### Aliases: note_in_html
> 
> ### ** Examples
> 
> note_in_html("Please write note using **Markdown** syntax! ")
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
Found the following significant warnings:
  ./SpecialFunctions.h:122:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:153:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:154:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:155:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:197:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:198:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/NPBayesImputeCat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/npcp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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 39-42 (downloading_data_nsrr.Rmd) 
Error: processing vignette 'downloading_data_nsrr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2Extras’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   9.9Mb
File ‘obliclus/libs/obliclus.so’:
  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 10.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
installed size is 77.3Mb
  sub-directories of 1Mb or more:
    libs  76.8Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OpenCL.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.3Mb
installed size is 156.8Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    146.8Mb
    models    4.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘org.At.tair.db’
Running ‘bdstest.R’ [1s/1s]
  Running ‘hobbs.R’ [4s/4s]
Running the tests in ‘tests/hobbs.R’ failed.
Last 13 lines of output:
  In kktchk(ans$par, fn, wgr, hess = NULL, upper = NULL, lower = NULL,  :
    Eigenvalue failure for projected Hessian
  This problem is unconstrained.
  Error in lbfgsb3::lbfgsb3(prm = spar, fn = efn, gr = egr, control = mcontrol,  : 
    NA/NaN/Inf in foreign function call (arg 7)
  In addition: Warning messages:
  1: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  2: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  3: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  4: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  libc++abi.dylib: terminating with uncaught exception of type std::range_error: non-finite x values not allowed in calfun
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/3.5/optiSel.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.2Mb
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘IsoGene’
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (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.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/osc.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.1Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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:
cannot open the connection
Execution halted
EAMM: no visible global function definition for ‘anova’
EAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘anova’
SSF: no visible global function definition for ‘rand’
SSF: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova rand
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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.
Linking to GEOS 3.6.1, GDAL 2.1.3, 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

Downloading constituency data
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]="./webshotbe8b43496a3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotbe8b43496a3.png': No such file or directory
Quitting from lines 65-108 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.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 ‘testthat.R’ [36s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L), .Label = c("setosa", "versicolor", "virginica"
     ), class = "factor", contrasts = "contr.dummy"), TRUE)
  18: get(ctr, mode = "function", envir = parent.frame())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 598 SKIPPED: 20 FAILED: 6
  1. Error: submodel prediction (@test_boost_tree_C50.R#113) 
  2. Error: stan prediction (@test_linear_reg_stan.R#57) 
  3. Error: stan intervals (@test_linear_reg_stan.R#105) 
  4. Error: stan intervals (@test_logistic_reg_stan.R#151) 
  5. Error: kknn prediction (@test_nearest_neighbor_kknn.R#95) 
  6. Error: (unknown) (@test_predict_formats.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘pathview’

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

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

Package which this enhances but not available for checking: ‘pmclust’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdPROF.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pcaL1.Rcheck/00install.out’ for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs    6.4Mb
    share  11.9Mb
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Peaks.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/permGPU.Rcheck/00install.out’ for details.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘PhenotypeSimulator.R’, ‘PhenotypeSimulator.Rmd’, ‘PhenotypeSimulator.html’, ‘PhenotypeSimulator.md’, ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
Error in re-building vignettes:
  ...
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]="./webshot19c9635f8145.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19c9635f8145.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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]="./webshot5cdc3ba9b84d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5cdc3ba9b84d.png': No such file or directory
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
* installing *source* package ‘milne’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (milne)

* installing *source* package ‘pkgnet’ ...
** package ‘pkgnet’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pkgnet)
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 77-113 (pkgnet-intro.Rmd) 
Error: processing vignette 'pkgnet-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Packages required but not available:
  ‘VariantAnnotation’ ‘Rsamtools’ ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
S3 methods shown with full name in documentation object 'rbind.fill':
  ‘rbind.fill’

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  ‘rbind.fill.matrix’

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  8.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.9Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘tidyr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 139-140 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polyPK.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

For example usage please run: vignette('qqman')

Citation appreciated but not required:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).

Quitting from lines 344-347 (polyRADtutorial.Rmd) 
Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
there is no package called 'VariantAnnotation'
Execution halted
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0      1.68      0.535           2 F    
 9            9         9    20      1      0.911    -0.555           2 F    
10           10        10    12      1      0.237     1.78            1 M    
# … with more rows

> library(VariantAnnotation)

  When sourcing ‘poplite.R’:
Error: there is no package called ‘VariantAnnotation’
Execution halted
Error in re-building vignettes:
  ...

    select

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

    filter

Error in makeSchemaFromData(dna, "dna") : 
  ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
Starting clinical
Starting samples
Starting dna
Warning: call dbDisconnect() when finished working with a connection
Error in filter_.Database(.data, .dots = compat_as_lazy_dots(...)) : 
  ERROR: Cannot uniquely map columns to table, try using: tableX.columnY
Starting gender
Starting clinical
Starting samples
Starting dna

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

> suppressMessages(library(ROI.plugin.quadprog))

> suppressMessages(library(ROI.plugin.glpk))

  When sourcing ‘ROI_vignette.R’:
Error: there is no package called ‘ROI.plugin.glpk’
Execution halted
when running code in ‘portfolio_vignette.Rnw’
  ...

> maxret <- add.objective(portfolio = init, type = "return", 
+     name = "mean")

> opt_maxret <- optimize.portfolio(R = R, portfolio = maxret, 
+     optimize_method = "ROI", trace = TRUE)

  When sourcing ‘portfolio_vignette.R’:
Error: paste0("package:", plugin) %in% search() || requireNamespace(plugin,  .... is not TRUE
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'ROI_vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.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/3.5/PPQplan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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: Ignoring unknown aesthetics: z
Warning: Ignoring unknown aesthetics: z
Warning in normalizePath(f2) :
  path[1]="./webshot1635920dad531.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1635920dad531.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/praznik.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/3.5/predict3d.Rcheck/00install.out’ for details.
Running ‘testthat-prediction.R’ [20s/21s]
Running the tests in ‘tests/testthat-prediction.R’ failed.
Last 13 lines of output:
  5: get_all_vars(model, data = env)
  6: as.formula(formula)
  7: formula(object, env = baseenv())
  8: formula.default(object, env = baseenv())
  9: stop("invalid formula")
  
  (Intercept)    tensionM    tensionH 
     36.38889   -10.00000   -14.72222 
  Using automatic sigma estimation (sigest) for RBF or laplace kernel 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 170 SKIPPED: 0 FAILED: 1
  1. Error: Test prediction() for 'bigLm' (@tests-methods.R#88) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Error in re-building vignettes:
  ...
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 31-44 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘parsnip’
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'probably'

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

    as.factor, as.ordered


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 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 29-45 (where-to-use.Rmd) 
Error: processing vignette 'where-to-use.Rmd' failed with diagnostics:
there is no package called 'parsnip'
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.1Mb
    htmlwidgets   2.5Mb
Error in re-building vignettes:
  ...

    intersect, setdiff, setequal, union

Loading required package: edeaR
Loading required package: eventdataR
Loading required package: processmapR
Loading required package: xesreadR
Loading required package: processmonitR
Loading required package: petrinetR

Attaching package: 'bupaR'

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

    filter

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

    timestamp

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 23-49 (use-external-data-to-change-tokens.Rmd) 
Error: processing vignette 'use-external-data-to-change-tokens.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      5.5Mb
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
Error in re-building vignettes:
  ...
The following object is masked from 'package:ggplot2':

    last_plot

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

    get_x, get_y

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

    filter

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

    layout

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]="./webshotdc086150611d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdc086150611d.png': No such file or directory
Quitting from lines 506-534 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ptinpoly.Rcheck/00install.out’ for details.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PWFSLSmoke.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PythonInR.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/3.5/qpcR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QPot.Rcheck/00install.out’ for details.
Found the following executable file:
  src/LZ4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qtbase.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   1.3Mb
    libs  10.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.2Mb
File ‘QUIC/libs/QUIC.so’:
  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/qVarSel.so’:
  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.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
Package suggested but not available for checking: ‘CGHbase’
Package unavailable to check Rd xrefs: ‘CGHbase’
Error in .requirePackage(package) : 
    unable to find required package 'CGHbase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   9.2Mb
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.5Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Package suggested but not available for checking: ‘rpanel’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   5.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘rattle’
Packages suggested but not available for checking:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2’
  ‘RGtk2Extras’
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  29.9Mb
Errors in running code in vignettes:
when running code in ‘rbiouml.Rnw’
  ...
filterExpression Expression in JavaScript like 'ColumnName1 > 5 && ColumnName2 < 0'
filteringMode                                                  Which rows to select
outputPath                                               Path to the filtered table

> biouml.analysis("Filter table", list(inputPath = "data/Examples/Optimization/Data/Experiments/exp_data_1", 
+     filterExpression = "time < 40", ou .... [TRUNCATED] 

  When sourcing ‘rbiouml.R’:
Error: Internal server error: java.lang.NullPointerException
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  Internal server error: java.lang.NullPointerException
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.2Mb
Package required but not available: ‘h5’

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/3.5/Rborist.Rcheck/00install.out’ for details.
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Error in re-building vignettes:
  ...
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 62-65 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rcplex.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
    libs      1.7Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppMeCab.Rcheck/00install.out’ for details.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      24.0Mb
    libs      8.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.5Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.2Mb
    libs      4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcrypt.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rdist.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in normalizePath(f2) :
  path[1]="./webshot94d2112788b9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot94d2112788b9.png': No such file or directory
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:
cannot open the connection
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.4Mb
Missing link or links in documentation object 'step_nnmf.Rd':
  ‘[dimRed:NNMF]{dimRed::NNMF()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  14.7Mb
Package required but not available: ‘GenomeGraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.4Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: Testing the introduction presentation (@test-SlideDeck.R#6)  ──────
  Please install either RStudio or Pandoc (https://pandoc.org)
  1: Read()$auto(tfname, quiet = TRUE) at testthat/test-SlideDeck.R:6
  2: get(fileExt, mode = "function")(fileName, ...)
  3: md(mdFile)
  4: knitr::pandoc(fileName, format = "plain")
  5: stop("Please install either RStudio or Pandoc (https://pandoc.org)")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error:  (@test-Evaluate.R#7) 
  2. Error: Testing the introduction presentation (@test-SlideDeck.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
S3 methods shown with full name in documentation object 'all.vars.character':
  ‘all.vars.character’

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 ‘restfulr_unit_tests.R’ [3m/28m]
Running the tests in ‘tests/restfulr_unit_tests.R’ failed.
Last 13 lines of output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/.local/share/R/rsolr/solr-undertow-1.5.0-RC1-with-solr-5.3.0/lib/xnio-nio-3.4.0.Beta1.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
  WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  
  Execution halted
  rm: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprsxEQD: Too many open files
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    libs      77.3Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
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/3.5/rgl.Rcheck/00install.out’ for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    3.7Mb
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

> ### Name: grmod
> ### Title: Interface for _gretl_ estimation commands
> ### Aliases: grmod
> 
> ### ** Examples
> 
> set.seed(13)
> dfr = data.frame(y = rnorm(20), x = rnorm(20))
> grmod("ols y 0 x --simple-print",dfr)

No valid gretl executable: no output is produced
Error: '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpNZE4NO/mbundle4ef27a0e3e9.xml' does not exist.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

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/3.5/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rise.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
Execution halted
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (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.
Package suggested but not available for checking: ‘golubEsets’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.2Mb
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmpi.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.3Mb
    libs      3.3Mb
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     93.7Mb
Packages required and available but unsuitable versions:
  ‘impute’ ‘MassSpecWavelet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/robfilter.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘beadarrayExampleData’ ‘illuminaHumanv3.db’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Package required but not available: ‘clpAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ROI.plugin.glpk’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ROracle.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.5Mb
S3 methods shown with full name in documentation object 'cbind.fill':
  ‘cbind.fill’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpanel.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpg.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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:
cannot open the connection
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rpoppler.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  11: stringr::str_trim
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 8 FAILED: 1
  1. Error: thisfile works with knitr (@test-thisfile.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.7Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

Package which this enhances but not available for checking: ‘rjpod’

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/3.5/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    dependencies  21.0Mb
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/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’

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.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘ctc’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 110.1Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    libs  107.1Mb
installed size is 230.5Mb
  sub-directories of 1Mb or more:
    libs  228.0Mb
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("rstpm2")
  ── 1. Failure: Predictions with missing values - pstpm2+frailty (@test_missing.R
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00142
  
  ── 2. Failure: Predictions with missing values - pstpm2+frailty (@test_missing.R
  max(abs(expr - value)) is not strictly less than `eps`. Difference: 0.00142
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 46 SKIPPED: 0 FAILED: 2
  1. Failure: Predictions with missing values - pstpm2+frailty (@test_missing.R#227) 
  2. Failure: Predictions with missing values - pstpm2+frailty (@test_missing.R#227) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rsymphony.Rcheck/00install.out’ for details.
Running ‘run_test.R’ [8s/8s]
Running the tests in ‘tests/run_test.R’ failed.
Last 13 lines of output:
  Linking to ImageMagick 6.9.9.39
  Enabled features: cairo, fontconfig, freetype, lcms, pango, rsvg, webp
  Disabled features: fftw, ghostscript, x11
  Loading required package: XML
  Thank you for using RTest
  
  To use a more comprehensive version of the test-report we recommend to run:
  
  assignInNamespace("as.expectation.logical", RTest::as.expectation.logical, ns="testthat", pos="package:testthat")
  Error: Test failed: 'RTestCollection write HTML summary'
  * `writeExecSummary.html(...)` produced warnings.
  * `writeExecSummary.html(...)` produced warnings.
  In addition: Warning message:
  In fun(libname, pkgname) : couldn't connect to display ":0"
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...
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]="./webshot185cf1e31ca10.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot185cf1e31ca10.png': No such file or directory
Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.8Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Running examples in ‘rviewgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: rViewGraph
> ### Title: This is a function to create and start the Java graph animation
> ###   GUI.
> ### Aliases: rViewGraph rViewGraph.default rViewGraph.Matrix
> ###   rViewGraph.igraph
> ### Keywords: graph
> 
> ### ** Examples
> 
> # 
> # Viewing an Erdos Renyui random graph specified by random edges.
> f = sample(100,size=200,replace=TRUE)
> t = sample(100,size=200,replace=TRUE)
> vft = rViewGraph(cbind(f,t))
Error in .jnew("rviewgraph/RViewGraph", v, f, t, x, y, directed, running) : 
  java.awt.HeadlessException
Calls: rViewGraph ... rViewGraph.default -> rViewGraphCore -> init -> .jnew
Execution halted
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs     43.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxCEcolInf.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs    6.3Mb
    yacas   1.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
Found the following significant warnings:
  dists.cc:4239:21: 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/3.5/SafeBayes.Rcheck/00install.out’ for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
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 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.5Mb
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SDMTools.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Packages required but not available: ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   6.9Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘made4’ ‘SingleCellExperiment’ ‘MAST’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 112.8Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    libs    97.6Mb
    sqlite   1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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/3.5/shapes.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    www   7.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot137275ec3b513.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot137275ec3b513.png': No such file or directory
Quitting from lines 26-42 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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:
cannot open the connection
Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.0Mb
Package required but not available: ‘BSgenome’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

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

Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   5.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SMCP.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.6Mb
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.9Mb
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 1.21 secs
Identifing all possible orderings..
Total run time: 0.86 secs
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]="./webshotf9064431846f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf9064431846f.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:RandomFieldsUtils':

    RFoptions

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

    abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
    expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
    round, sin, sinh, sqrt, tan, tanh, trunc

Setting:
  options(
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    reproducible.cachePath = '/private/tmp/RtmpblkGAL/reproducible/cache'
    spades.inputPath = '/private/tmp/RtmpP9tEJ9/SpaDES/inputs'
    spades.outputPath = '/private/tmp/RtmpP9tEJ9/SpaDES/outputs'
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Quitting from lines 376-382 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  28.4Mb
Error in re-building vignettes:
  ...
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]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   9.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.8Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Packages required but not available: ‘xcms’ ‘MAIT’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.5Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    lib       1.6Mb
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Files identified: dftRoadSafetyData_Casualties_2017.zip

   http://data.dft.gov.uk.s3.amazonaws.com/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip
Attempt downloading from: 
trying URL 'http://data.dft.gov.uk.s3.amazonaws.com/road-accidents-safety-data/dftRoadSafetyData_Casualties_2017.zip'
Content type 'application/x-zip-compressed' length 1169376 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Data saved at /tmp/RtmpSnIBKR/dftRoadSafetyData_Casualties_2017/Cas.csv
Files identified: dftRoadSafetyData_Vehicles_2017.zip

   http://data.dft.gov.uk.s3.amazonaws.com/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2017.zip
Attempt downloading from: 
trying URL 'http://data.dft.gov.uk.s3.amazonaws.com/road-accidents-safety-data/dftRoadSafetyData_Vehicles_2017.zip'
Content type 'application/x-zip-compressed' length 2584589 bytes (2.5 MB)
==================================================
downloaded 2.5 MB

Data saved at /tmp/RtmpSnIBKR/dftRoadSafetyData_Vehicles_2017/Veh.csv
Joining, by = "accident_index"
Quitting from lines 256-267 (blog.Rmd) 
Error: processing vignette 'blog.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxchi
> ### Title: Stepwise detection of recombination breakpoints using MaxChi
> ### Aliases: maxchi
> ### Keywords: htest
> 
> ### ** Examples
>  demo(maxchi) 


	demo(maxchi)
	---- ~~~~~~

> inputFile<- system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(531,616,810)

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stream.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.4Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package required but not available: ‘ShortRead’

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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.
sh: line 1: 13800 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/Rtmp3Fs7ok/x1335e058a2e03f/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x122fb2579
#1  0x122fb1945
#2  0x7fff93ac4529
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

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/3.5/stUPscales.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  dists.cc:4239:21: 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/3.5/SuppDists.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  80.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' 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/3.5/svd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘svHttp’
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_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’

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: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  14.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.3Mb
    tessdata  14.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Running examples in ‘threejs-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphjs
> ### Title: Interactive 3D Graph Visualization
> ### Aliases: graphjs
> 
> ### ** Examples
> 
> set.seed(1)
> g <- sample_islands(3, 10, 5/10, 1)
> i <- cluster_optimal(g)
Error in cluster_optimal(g) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Execution halted
Package required but not available: ‘parsnip’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Error in re-building vignettes:
  ...
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: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
Error in re-building vignettes:
  ...
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: sp
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 208-214 (tiler.Rmd) 
Error: processing vignette 'tiler.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 685 SKIPPED: 0 FAILED: 3
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
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/3.5/tkrplot.Rcheck/00install.out’ for details.
Warning: loading Rplot failed

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 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, 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.
Error in re-building vignettes:
  ...
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:
cannot open the connection
Execution halted
Running ‘testthat.R’ [18s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tractor.base)
  > 
  > test_check("tractor.base")
  ── 1. Failure: file functions work (@test-30-misc.R#28)  ───────────────────────
  imageFileExists(temp) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: file functions work (@test-30-misc.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.1Mb
Error in re-building vignettes:
  ...
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:
cannot open the connection
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/3.5/trinROC.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 23, 2018 11:16:19 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:20 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TSdbi
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.util.Configuration init
INFO: No configuration found. Apply defaults.
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:29 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN%2BUSA%2BMEX.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.4Mb
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: getTSE
> ### Title: Download Historical Dataset from Tehran Stock Exchange (TSE)
> ### Aliases: getTSE
> 
> ### ** Examples
> 
> 	fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> 	assets0<-getTSE(fpath)$assets
proceeding...
Warning in download.file(temp, file1, mode = "wb", quiet = TRUE) :
  URL 'http://www.tsetmc.com/tsev2/data/Export-txt.aspx?t=i&a=1&b=0&i=39453972158399542': status was 'Couldn't connect to server'
Error in download.file(temp, file1, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://www.tsetmc.com/tsev2/data/Export-txt.aspx?t=i&a=1&b=0&i=39453972158399542'
Calls: getTSE -> download.file
Execution halted
Error in re-building vignettes:
  ...
          separate plot or all together c("single, "multiple)

  Xtitle: A character, set the X axis title, default set to NULL

  Ytitle: A character, set the Y axis title, default set to NULL

   title: A character, set the plot title, default set to NULL

   Xgrid: Logic,show the X axis grid if set to TRUE

   Ygrid: Logic,show the Y axis grid if set to TRUE

_E_x_a_m_p_l_e_s:

     data(USVSales)
     ts_plot(USVSales)
     
     # adding slider
     ts_plot(USVSales, slider = TRUE)
     

Quitting from lines 43-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
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/3.5/TukeyRegion.Rcheck/00install.out’ for details.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.0Mb
Error in re-building vignettes:
  ...
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

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]="./webshot6b661ba5942.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6b661ba5942.png': No such file or directory
Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  test small
  
  test_spectral
  
  test_synthetic
  
  test_universal
  
  test_utils
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 206 SKIPPED: 0 FAILED: 1
  1. Failure: predicted layout is reasonable (@test_naive.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported object: ‘devtools::check_rhub’
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Error in re-building vignettes:
  ...
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: magic
Loading required package: abind

     PLEASE NOTE:  As of version 0.3-5, no degenerate (zero area) 
     regions are returned with the "Qt" option since the R 
     code removes them from the triangulation. 
     See help("delaunayn").


Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.6Mb
    libs   3.5Mb
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’

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  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 79.0Mb
  sub-directories of 1Mb or more:
    libs  77.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    doc    1.2Mb
    help   2.8Mb
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘ggplot2’ in library.dynam(lib, package, package.lib):
 shared object ‘Rcpp.so’ not found
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
File ‘waffect/libs/waffect.so’:
  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 56.9Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  54.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wand.Rcheck/00install.out’ for details.
Package required but not available: ‘bioacoustics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: curl::curl_echo(h) at testthat/test-echo.R:14
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ── 2. Error: Echo a big file (@test-echo.R#51)  ────────────────────────────────
  Callback aborted
  1: curl::curl_echo(h) at testthat/test-echo.R:51
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Error: test echo from httpuv (@test-echo.R#14) 
  2. Error: Echo a big file (@test-echo.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
Package suggested but not available for checking: ‘org.Mm.eg.db’
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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Running ‘testthat.R’ [38s/42s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  7: value[[3L]](cond)
  8: stop(e$message, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 833 SKIPPED: 116 FAILED: 6
  1. Failure: obtain_existing_paths works when the root is the upstream existing directory (unix-like) (@test-obtain_existing_path.R#64) 
  2. Failure: obtain_existing_paths works when the root is the upstream existing directory (unix-like) (@test-obtain_existing_path.R#65) 
  3. Failure: obtain_existing_paths works when the root is the upstream existing directory (unix-like) (@test-obtain_existing_path.R#66) 
  4. Failure: obtain_existing_paths works when the root is the upstream existing directory (unix-like) (@test-obtain_existing_path.R#67) 
  5. Failure: obtain_existing_paths works when the root is the upstream existing directory (unix-like) (@test-obtain_existing_path.R#68) 
  6. Error: wflow_use_github can be used post GitLab (@test-wflow_use_github.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking: ‘GenomicScores’ ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'modification.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ZipRadius.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.1Mb
    libs                    3.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/ACTCD.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/AdaptGauss.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
Running examples in 'ahaz-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.tune.ahazpen
> ### Title: Prediction methods for tune.ahazpen
> ### Aliases: predict.tune.ahazpen coef.tune.ahazpen
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(sorlie)
> 
> set.seed(10101)
> 
> # Break ties
> time <- sorlie$time+runif(nrow(sorlie))*1e-2
> 
> # Survival data + covariates
> surv <- Surv(time,sorlie$status)
> X <- as.matrix(sorlie[,3:ncol(sorlie)])
> 
> # Fit additive hazards regression model w/lasso penalty
> cv.fit <- tune.ahazpen(surv, X, dfmax=100, tune="cv")
> 
> # Predict coefficients at cv.fit$lambda.min
> coef(cv.fit)
549 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/alphahull.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Missing or unexported object: 'rhdf5::h5closeAll'
Package required but not available: 'BiocManager'

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

> ### Name: conversions
> ### Title: Conversions Between Dense and Sparse Similarity Matrices
> ### Aliases: conversions as.SparseSimilarityMatrix as.DenseSimilarityMatrix
> ###   as.SparseSimilarityMatrix-methods as.DenseSimilarityMatrix-method
> ###   as.SparseSimilarityMatrix,matrix-method
> ###   as.DenseSimilarityMatrix,matrix-method
> ###   as.SparseSimilarityMatrix,sparseMatrix-method
> ###   as.DenseSimilarityMatrix,sparseMatrix-method
> ###   as.SparseSimilarityMatrix,Matrix-method
> ###   as.DenseSimilarityMatrix,Matrix-method
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## create similarity matrix in sparse format according to Frey and Dueck
> sp <- matrix(c(1, 2, 0.5, 3, 1, 0.2, 5, 4, -0.2, 3, 4, 1.2), 4, 3, byrow=TRUE)
> sp
     [,1] [,2] [,3]
[1,]    1    2  0.5
[2,]    3    1  0.2
[3,]    5    4 -0.2
[4,]    3    4  1.2
> 
> ## perform conversions
> as.DenseSimilarityMatrix(sp, fill=0)
     [,1] [,2] [,3] [,4] [,5]
[1,]  0.0  0.5    0  0.0    0
[2,]  0.0  0.0    0  0.0    0
[3,]  0.2  0.0    0  1.2    0
[4,]  0.0  0.0    0  0.0    0
[5,]  0.0  0.0    0 -0.2    0
> as.SparseSimilarityMatrix(sp)
5 x 5 sparse Matrix of class "dgTMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Running examples in 'arulesSequences-Ex.R' failed
The error most likely occurred in:

> ### Name: similarity-methods
> ### Title: Compute Similarities
> ### Aliases: similarity similarity,sequences-method is.subset
> ###   is.subset,sequences-method is.superset is.superset,sequences-method
> ###   coerce,dsCMatrix,dist-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## use example data
> data(zaki)
> z <- as(zaki, "timedsequences")
> similarity(z)
4 x 4 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(atlantistools)
  > 
  > test_check("atlantistools")
  -- 1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  dim(df1) not equal to c(4, 16).
  1/2 mismatches
  [1] 5 - 4 == 1
  
  -- 2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$linf[3] not equivalent to 87.4.
  1/1 mismatches
  [1] 75.1 - 87.4 == -12.3
  
  -- 3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$k[2] not equivalent to 0.15.
  1/1 mismatches
  [1] 0.53 - 0.15 == 0.38
  
  -- 4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase
  df1$locality[1] not equivalent to "Central Adriatic, 100-200 m depth".
  1/1 mismatches
  x[1]: "northeast Mediterranean Sea"
  y[1]: "Central Adriatic, 100-200 m depth"
  
  == testthat results  ===========================================================
  OK: 193 SKIPPED: 1 FAILED: 4
  1. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#6) 
  2. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#7) 
  3. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#8) 
  4. Failure: test extraction for Small-spotted catshark (@test-growth-fishbase.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/audio.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'BiocManager'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   1.9Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In cmpSym(e, cb, cntxt, missingOK) :
    closing unused connection 3 (http://www.fangraphs.com/guts.aspx?type=cn)
  Execution halted
Running 'Bernstein-Ex.R' [4s]
  Running 'bases-Ex.R' [9s]
  Running 'formula.R' [3s]
Running the tests in 'tests/formula.R' failed.
Complete output:
  > 
  > library("basefun")
  Loading required package: variables
  > 
  > n <- 100
  > x <- runif(n)
  > y <- runif(n)
  > g <- gl(4, n / 4)
  > d <- data.frame(y = y, x = x, g = g)
  > de <- d[-(1:nrow(d)),]
  > 
  > b1 <- as.basis(~ x + g, data = d)
  > b2 <- Bernstein_basis(numeric_var("y", support = c(0.0, 1.0)), 
  +                       order = 4, ui = "incre")
  > 
  > b12 <- b(b1 = b1, b2 = b2)
  > c12 <- c(b1 = b1, b2 = b2)
  > 
  > X1 <- model.matrix(b(b2 = b2, b1 = b1), data = d)
  > X2 <- model.matrix(b(b2 = b2, b1 = b1, sumconstr = TRUE), data = d)
  > all.equal(X1[,], X2[,])
  [1] TRUE
  > attr(X1, "constraint")$ui
  45 x 25 sparse Matrix of class "dgCMatrix"
  Error in isFALSE(suppRows) : could not find function "isFALSE"
  Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
  Execution halted
Running 'Bernstein-Ex.R' [4s]
  Running 'bases-Ex.R' [11s]
  Running 'formula.R' [4s]
Running the tests in 'tests/formula.R' failed.
Complete output:
  > 
  > library("basefun")
  Loading required package: variables
  > 
  > n <- 100
  > x <- runif(n)
  > y <- runif(n)
  > g <- gl(4, n / 4)
  > d <- data.frame(y = y, x = x, g = g)
  > de <- d[-(1:nrow(d)),]
  > 
  > b1 <- as.basis(~ x + g, data = d)
  > b2 <- Bernstein_basis(numeric_var("y", support = c(0.0, 1.0)), 
  +                       order = 4, ui = "incre")
  > 
  > b12 <- b(b1 = b1, b2 = b2)
  > c12 <- c(b1 = b1, b2 = b2)
  > 
  > X1 <- model.matrix(b(b2 = b2, b1 = b1), data = d)
  > X2 <- model.matrix(b(b2 = b2, b1 = b1, sumconstr = TRUE), data = d)
  > all.equal(X1[,], X2[,])
  [1] TRUE
  > attr(X1, "constraint")$ui
  45 x 25 sparse Matrix of class "dgCMatrix"
  Error in isFALSE(suppRows) : could not find function "isFALSE"
  Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.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:
> study_details(total_sample_size = 300, study_period = 50, interim_look = c(210, 240, 270))
$N_total
[1] 300

$EndofStudy
[1] 50

$interim_look
[1] 210 240 270

$prop_loss_to_followup
[1] 0.1

> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  10.81 0.22 11.05 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  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   4.0Mb
Running 'run_tests.R' [23s]
  Running 'test_functions.R' [2s]
Running the tests in 'tests/test_functions.R' failed.
Complete output:
  > library(bayesPop)
  Loading required package: bayesTFR
  Loading required package: bayesLife
  Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
  Error: package or namespace load failed for 'bayesPop' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
  Execution halted
Running 'run_tests.R' [3s]
Running the tests in 'tests/run_tests.R' failed.
Complete output:
  > library(bayesPop)
  Loading required package: bayesTFR
  Loading required package: bayesLife
  Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
  Error: package or namespace load failed for 'bayesPop' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
  Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'baytrends'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Running examples in 'baytrends-Ex.R' failed
The error most likely occurred in:

> ### Name: gamDiff
> ### Title: Compute an estimate of difference based on GAM results
> ### Aliases: gamDiff
> 
> ### ** Examples
> 
> # run analysisOrganizeData function to create the list analySpec
> dfr <- analysisOrganizeData (dataCensored, report=NA)
> df        <- dfr[["df"]]
> analySpec <- dfr[["analySpec"]]
> 
> # set GAM models to just one model
> analySpec$gamModels <- list(
+   list(option=2, name= "Non-linear trend with Seasonality (plus Interactions)",
+        model= "~ cyear + s(cyear) + s(doy,bs='cc')+ ti(cyear,doy,bs=c('tp','cc'))", deriv=FALSE))
> 
> # run GAM for a single water quality variable, station and layer
> gamResult <- gamTest(df, 'tn', 'CB5.4', 'S', analySpec=analySpec)
Error in stri_sub(string, from = start, to = end, omit_na = omit_na) <- value : 
  cannot open file 'D:/temp/RtmpAFGDQs/RLIBS_5d941f3c7db9/stringi/R/stringi.rdb': No such file or directory
Calls: gamTest ... mapply -> <Anonymous> -> .substitute_formats -> str_sub<-
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'create_Seasonally_Detrended_Flow_and_Salinity_Data_Sets.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup
Execution halted
Running examples in 'BDgraph-Ex.R' failed
The error most likely occurred in:

> ### Name: bdgraph.mpl
> ### Title: Search algorithm in graphical models using marginal
> ###   pseudo-likehlihood
> ### Aliases: bdgraph.mpl
> 
> ### ** Examples
> 
> # Generating multivariate normal data from a 'random' graph
> data.sim <- bdgraph.sim( n = 70, p = 5, size = 7, vis = TRUE )
>    
> bdgraph.obj <- bdgraph.mpl( data = data.sim, iter = 500 )
500 iteration is started.                     
>   
> summary( bdgraph.obj )
$selected_g
5 x 5 sparse Matrix of class "dtCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'cba_macsplex_example.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_
Execution halted
Package required and available but unsuitable version: 'ufs'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'berryFunctions.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Running examples in 'BeSS-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.bess
> ### Title: Provides estimated coefficients from a fitted "bess" object.
> ### Aliases: coef.bess
> 
> ### ** Examples
> 
> 
> data <- gen.data(500, 20, family = "gaussian", 10, 0.2, 1)
> fit <- bess(data$x, data$y, family = "gaussian")
> coef(fit, sparse=TRUE)  # The estimated coefficients
21 x 6 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'bhrcr-tutorial.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: as_glue, backtick, double_quote, glue, glue_col, glue_collapse, glue_data, glue_data_col, glue_data_sql, glue_sql, identity_transformer, single_quote, trim
In addition: Warning messages:
1: S3 methods '+.glue', '[.glue', '[[.glue', 'as.character.glue', 'as_glue.character', 'as_glue.default', 'as_glue.glue', 'print.glue' were declared in NAMESPACE but not found 
2: S3 methods '+.glue', '[.glue', '[[.glue', 'as.character.glue', 'as_glue.character', 'as_glue.default', 'as_glue.glue', 'print.glue' were declared in NAMESPACE but not found 
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: <Anonymous>
Execution halted
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'bibliometrix-Ex.R' failed
The error occurred in:


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 <- "bibliometrix"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('bibliometrix')
Error: package or namespace load failed for 'bibliometrix' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'bibliometrix-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated
Execution halted
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'bigQueryR.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Running examples in 'BigQuic-Ex.R' failed
The error most likely occurred in:

> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), 
+                          outputFileName = tempfile(pattern = 
+                          "BigQuic_output_matrix", fileext = ".Bmat"),
+                          lambda = lambda, numthreads = 1, memory_size = 512, 
+                          seed = 1, use_ram = TRUE)
> BigQuic.select(exampleResult)
Reference class object of class "BigQuic_object"
Field "precision_matrices":
[[1]]
200 x 200 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'binGroup' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'binneR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/BiodiversityR.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'biogeo' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'overview.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'biomartr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Running 'testthat.R' [269s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BIOMASS)
  > 
  > test_check("BIOMASS")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  -- 1. Failure: CorrectTaxo (@test_00_correctTaxo.R#79)  ------------------------
  correctTaxo(...) not equal to data.frame(...).
  Component "genusCorrected": 1 string mismatch
  Component "speciesCorrected": 1 string mismatch
  Component "nameModified": 1 string mismatch
  
  == testthat results  ===========================================================
  OK: 502 SKIPPED: 0 FAILED: 1
  1. Failure: CorrectTaxo (@test_00_correctTaxo.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/biomod2.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.6Mb
Loading this package had a fatal error status code 1
Loading log:
Loading required package: pkgconfig
Error: package or namespace load failed for 'biospear' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Running examples in 'bipartiteD3-Ex.R' failed
The error most likely occurred in:

> ### Name: Array2DF
> ### Title: Convert bipartite-style arrays to dataframe
> ### Aliases: Array2DF
> 
> ### ** Examples
> 
> data(Safariland, vazquenc, package='bipartite')
> allin1 <- bipartite::webs2array(Safariland, vazquenc)
> Array2DF(allin1)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: Array2DF ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'bipartiteD3_Intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/blockseg.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'blorr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
** DONE
Running examples in 'bmlm-Ex.R' failed
The error most likely occurred in:

> ### Name: mlm_path_plot
> ### Title: Plot 'bmlm"s mediation model as a path diagram
> ### Aliases: mlm_path_plot
> 
> ### ** Examples
> 
> # Draw a template path diagram of the mediation model
> mlm_path_plot()
Error: qgraph package needed for this function. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'methods.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'bnstruct.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'boxr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_de
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 210-214 (BradleyTerryScalable.Rmd) 
Error: processing vignette 'BradleyTerryScalable.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'breathtestcore' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'adding-tidiers.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'brranching' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs
Error: package or namespace load failed for 'bsam' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupli
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'bulletr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_du
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'examples.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cansim.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'using_captr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Test_Functions.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tests_and_coverage.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_an
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'cartools.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "modbin-unemployment1.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'modbin-unemployment1'. The following files exist in directory '.': 'altbin-teratology.Rnw', 'altbin-teratology.aux', 'altbin-teratology.log', 'altbin-teratology.pdf', 'altbin-teratology.tex', 'binary-unemployment.Rnw', 'binary-unemployment.aux', 'binary-unemployment.log', 'binary-unemployment.pdf', 'binary-unemployment.tex', 'binary-vaso.Rnw', 'binary-vaso.aux', 'binary-vaso.log', 'binary-vaso.pdf', 'binary-vaso.tex', 'count-children.Rnw', 'count-children.aux', 'count-children.log', 'count-children.pdf', 'count-children.tex', 'count-encephalitis.Rnw', 'count-encephalitis.aux', 'count-encephalitis.log', 'count-encephalitis.pdf', 'count-encephalitis.tex', 'count-insolvency.Rnw', 'count-insolvency.aux', 'count-insolvency.log', 'count-insolvency.pdf', 'count-insolvency.tex', 'count-medcare.Rnw', 'count-medcare.aux', 'count-medcare.log', 'count-medcare.pdf', 'count-medcare.tex', 'disc_c
Calls: buildVignettes -> find_vignette_product
Execution halted
Running examples in 'CatEncoders-Ex.R' failed
The error most likely occurred in:

> ### Name: OneHotEncoder.fit
> ### Title: OneHotEncoder.fit fits an OneHotEncoder object
> ### Aliases: OneHotEncoder.fit
> 
> ### ** Examples
> 
> # matrix input
> X1 <- matrix(c(0, 1, 0, 1, 0, 1, 2, 0, 3, 0, 1, 2),c(4,3),byrow=FALSE)
> oenc <- OneHotEncoder.fit(X1)
> z <- transform(oenc,X1,sparse=TRUE)
> # return a sparse matrix
> print(z)
4 x 9 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'amazon_s3_keys.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cdparcoord.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: ggplot2
Loading required package: gower
Error: package or namespace load failed for 'ceterisParibus' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, 
Execution halted
Running examples in 'cgmanalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: cgmreport
> ### Title: Generate AGP
> ### Aliases: cgmreport
> 
> ### ** Examples
> 
> cgmreport(system.file("extdata","Cleaned",package = "cgmanalysis"))
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: cgmreport ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Missing or unexported object: 'utils::askYesNo'
changer: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Error in re-building vignettes:
  ...
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Package suggested but not available for checking: 'ChemoSpec2D'
Error in re-building vignettes:
  ...
Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
Running examples in 'chillR-Ex.R' failed
The error most likely occurred in:

> ### Name: make_daily_chill_plot2
> ### Title: Plot daily climate metric accumulation throughout the year (2)
> ### Aliases: make_daily_chill_plot2
> ### Keywords: utility
> 
> ### ** Examples
> 
> 
> 
> daily<-daily_chill(stack_hourly_temps(fix_weather(
+   KA_weather[which(KA_weather$Year>2005),])),running_mean=11)
> 
> make_daily_chill_plot2(daily,metrics=c("Chill_Portions","GDH"),cumulative=TRUE,
+    startdate=300,enddate=30,focusyears=c(2009,2008))
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: make_daily_chill_plot2 ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'hourly_temperatures.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_a
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'duplicate.missing.cases.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicat
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'cimir' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'civis' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ck37r' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'poligrams.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Running examples in 'classyfireR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_classification
> ### Title: Get Entity Classification
> ### Aliases: get_classification
> 
> ### ** Examples
> 
> 
> # Valid InChI key where all four classification levels are available
> get_classification('BRMWTNUJHUMWMS-LURJTMIESA-N')
> 
> # Valid InChI key where only three classification levels are available
> get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-N')
> 
> # Invalid InChI key
> get_classification('MDHYEMXUFSJLGV-UHFFFAOYSA-B')
> 
> 
> # Using `dplyr` a vector of InChI Keys can be submitted and easily parsed
>   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(purrr)

Attaching package: 'purrr'

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

    set_names

>   library(tidyr)

Attaching package: 'tidyr'

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

    extract

> 
>  keys <- c(
+ 'BRMWTNUJHUMWMS-LURJTMIESA-N',
+ 'XFNJVJPLKCPIBV-UHFFFAOYSA-N',
+ 'TYEYBOSBBBHJIV-UHFFFAOYSA-N',
+ 'AFENDNXGAFYKQO-UHFFFAOYSA-N',
+ 'WHEUWNKSCXYKBU-QPWUGHHJSA-N',
+ 'WHBMMWSBFZVSSR-GSVOUGTGSA-N')
> 
>  classification_list <- map(keys, get_classification)
> 
>  classification_list <- map(classification_list, ~{select(.,-CHEMONT)})
Error in UseMethod("select_") : 
  no applicable method for 'select_' applied to an object of class "NULL"
Calls: map -> .Call -> .f -> select -> select.default -> select_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'clhs' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupli
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'cliapp' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Running examples in 'clustRcompaR-Ex.R' failed
The error most likely occurred in:

> ### Name: cluster
> ### Title: Cluster wrapper function
> ### Aliases: cluster
> 
> ### ** Examples
> 
> library(clustRcompaR)
> 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(quanteda)
Error: package or namespace load failed for 'quanteda' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustRcompaR)
  
  Attaching package: 'clustRcompaR'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > library(quanteda)
  Error: package or namespace load failed for 'quanteda' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction-to-clustRcompaR.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cocorresp-intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Running examples in 'codebook-Ex.R' failed
The error most likely occurred in:

> ### Name: add_R
> ### Title: Append R to string, if it doesn't end in R already.
> ### Aliases: add_R
> 
> ### ** Examples
> 
> data('bfi')
> bfi %>% dplyr::select(BFIK_open_2,BFIK_agree_2) %>% dplyr::rename_at(1, add_R) %>% head()
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'codebook.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'codemetar' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'nih-enrollment-html.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_a
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'binning-methods.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'noise.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'colorfindr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'colorspace.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'colorSpec-guide.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    app   2.7Mb
    doc   2.3Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'compboost.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'congressbr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'identify_sepsis.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cmabs.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/cooccur.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Functions or methods with usage in documentation object 'gasoil' but not in code:
  data

Functions or methods with usage in documentation object 'loss' but not in code:
  data

Functions or methods with usage in documentation object 'rdj' but not in code:
  data

Functions or methods with usage in documentation object 'uranium' but not in code:
  data
Undocumented arguments in documentation object 'gasoil'
  'gasoil' 'package'
Objects in \usage without \alias in documentation object 'gasoil':
  'data'

Undocumented arguments in documentation object 'loss'
  'loss' 'package'
Objects in \usage without \alias in documentation object 'loss':
  'data'

Undocumented arguments in documentation object 'rdj'
  'rdj' 'package'
Objects in \usage without \alias in documentation object 'rdj':
  'data'

Undocumented arguments in documentation object 'uranium'
  'uranium' 'package'
Objects in \usage without \alias in documentation object 'uranium':
  'data'

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 in re-building vignettes:
  ...
Error: processing vignette 'Using_coreCT.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Running examples in 'corpus-Ex.R' failed
The error most likely occurred in:

> ### Name: term_matrix
> ### Title: Term Frequency Tabulation
> ### Aliases: term_counts term_matrix
> 
> ### ** Examples
> 
> text <- c("A rose is a rose is a rose.",
+           "A Rose is red, a violet is blue!",
+           "A rose by any other name would smell as sweet.")
> term_matrix(text)
3 x 17 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'corpustools-Ex.R' failed
The error most likely occurred in:

> ### Name: as.tcorpus.tCorpus
> ### Title: Force an object to be a tCorpus class
> ### Aliases: as.tcorpus.tCorpus
> 
> ### ** Examples
> 
> tc = create_tcorpus(c('First text', 'Second text'))
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: create_tcorpus ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'countyweather.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'covatest' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'axis_position.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cowsay_tutorial.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'cranly' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'crimedata' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'crosswalkr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Running examples in 'crqanlp-Ex.R' failed
The error most likely occurred in:

> ### Name: clean_text
> ### Title: Clean text
> ### Aliases: clean_text
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> library(gutenbergr)
> ## let's get Alice's Adventures in Wonderland by Carroll
> # gutenberg_works(author == "Carroll, Lewis") 
> rawText = gutenberg_download(11) ## take the text
Determining mirror for Project Gutenberg from http://www.gutenberg.org/robot/harvest
`curl` package not installed, falling back to using `url()`
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: gutenberg_download ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'crsra' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'async.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: rvest
Loading required package: xml2
Error: package or namespace load failed for 'crypto' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.0Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'Roadmap.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc
Execution halted
Running examples in 'CVXR-Ex.R' failed
The error most likely occurred in:

> ### Name: Int-class
> ### Title: The Int class.
> ### Aliases: Int-class .Int Int as.character,Int-method
> ###   canonicalize,Int-method
> 
> ### ** Examples
> 
> x <- Int(3, name = "i") ## 3-int variable
> y <- Int(3, 3, name = "j") # Matrix variable
> as.character(y)
[1] "Int(3, 3)"
> id(y)
[1] 9
> is_positive(x)
[1] FALSE
> is_negative(x)
[1] FALSE
> size(y)
[1] 3 3
> name(y)
[1] "j"
> value(y) <- matrix(1:9, nrow = 3)
> value(y)
     [,1] [,2] [,3]
[1,]    1    4    7
[2,]    2    5    8
[3,]    3    6    9
> grad(y)
$`9`
9 x 9 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated
Execution halted
Running examples in 'cyclestreets-Ex.R' failed
The error most likely occurred in:

> ### Name: json2sf_cs
> ### Title: Convert output from CycleStreets.net into sf object
> ### Aliases: json2sf_cs
> 
> ### ** Examples
> 
> from = "Leeds Rail Station"
> to = "University of Leeds"
> # save result from the API call to journey.json
> # res_json = stplanr::route_cyclestreet(from, to, silent = FALSE, save_raw = TRUE)
> # jsonlite::write_json(res_json, "inst/extdata/journey.json")
> f = system.file(package = "cyclestreets", "extdata/journey.json")
> obj = jsonlite::read_json(f, simplifyVector = TRUE)
> rsf = json2sf_cs(obj)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: json2sf_cs ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cytominer-pipeline.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_an
Execution halted
Running examples in 'datapackage.r-Ex.R' failed
The error most likely occurred in:

> ### Name: Package.load
> ### Title: Instantiate 'Data Package' class
> ### Aliases: Package.load
> 
> ### ** Examples
> 
> 
> # Load local descriptor
> descriptor <- system.file('extdata/dp1/datapackage.json', 
+                          package = "datapackage.r")
> dataPackage <- Package.load(descriptor)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: Package.load ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'creating_data_packages_in_r.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'datapack' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'how-to-datapasta.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any,
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dataRetrieval' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'AdvancedVignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Introduction_to_datasus.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicat
Execution halted
Running 'autoprint.R' [1s]
  Comparing 'autoprint.Rout' to 'autoprint.Rout.save' ... OK
  Running 'froll.R' [14s]
  Running 'knitr.R' [1s]
Running the tests in 'tests/knitr.R' failed.
Complete output:
  > if (suppressPackageStartupMessages(requireNamespace("knitr", quietly = TRUE))) {
  +     require(knitr)
  +     knit("knitr.Rmd", quiet=TRUE)
  +     cat(readLines("knitr.md"), sep="\n")
  + } else {
  +     cat(readLines("knitr.Rout.mock", warn = FALSE), sep="\n")
  + }
  Loading required package: knitr
  Error in namespaceExport(ns, exports) : 
    undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
  Calls: knit ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Running 'autoprint.R' [1s]
  Comparing 'autoprint.Rout' to 'autoprint.Rout.save' ... OK
  Running 'froll.R' [16s]
  Running 'knitr.R' [1s]
Running the tests in 'tests/knitr.R' failed.
Complete output:
  > if (suppressPackageStartupMessages(requireNamespace("knitr", quietly = TRUE))) {
  +     require(knitr)
  +     knit("knitr.Rmd", quiet=TRUE)
  +     cat(readLines("knitr.md"), sep="\n")
  + } else {
  +     cat(readLines("knitr.Rout.mock", warn = FALSE), sep="\n")
  + }
  Loading required package: knitr
  Error in namespaceExport(ns, exports) : 
    undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
  Calls: knit ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'datatable-benchmarking.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicate
Execution halted
ClassMDplot: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'DataVisualizations-Ex.R' failed
The error most likely occurred in:

> ### Name: ClassMDplot
> ### Title: Class MD-plot for Data w.r.t. all classes
> ### Aliases: ClassMDplot
> 
> ### ** Examples
> 
> ## Don't show: 
> data(ITS)
> #clustering only for testing
> Classification=c(rep(1,8805),rep(2,2389))
> DataVisualizations::ClassMDplot(ITS,Classification)
Error in isFALSE(PlotLegend) : could not find function "isFALSE"
Calls: <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'query.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
Running examples in 'dcGOR-Ex.R' failed
The error most likely occurred in:

> ### Name: Ancestral_domainome
> ### Title: Ancestral superfamily domain repertoires in Eukaryotes
> ### Aliases: Ancestral_domainome
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Ancestral_domainome)
> Ancestral_domainome
An object of S4 class 'Anno'
@annoData: 2019 domains, 875 terms 
@termData (InfoDataFrame)
  termNames: 3 4 5 ... 1743 1750 (875 total)
  tvarLabels: left_id right_id taxon_id ... branchlength common_name (8
    total)
@domainData (InfoDataFrame)
  domainNames: 46458 46548 46557 ... 161266 161270 (2019 total)
  dvarLabels: sunid level classification description
> # retrieve info on terms/genomes
> termData(Ancestral_domainome)
An object of S4 class 'InfoDataFrame'
  rowNames: 3 4 5 ... 1743 1750 (875 total)
  colNames: left_id right_id taxon_id ... branchlength common_name (8
    total)
> # retrieve info on SCOP domains
> domainData(Ancestral_domainome)
An object of S4 class 'InfoDataFrame'
  rowNames: 46458 46548 46557 ... 161266 161270 (2019 total)
  colNames: sunid level classification description
> # retrieve the first 5 rows and columns of data
> x <- annoData(Ancestral_domainome)[1:5,1:5]
> x
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'algorithm.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'arc-layer.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'Cluster_Analysis.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any,
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'desplot' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_du
Execution halted
Running examples in 'dglars-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.cvdglars
> ### Title: Extract the Coefficients Estimated by 'cvdglars'
> ### Aliases: coef.cvdglars
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ###########################
> # Logistic regression model
> set.seed(123)
> n <- 100
> p <- 10
> X <- matrix(rnorm(n * p), n, p)
> b <- 1:2
> eta <- b[1] + X[,1] * b[2]
> mu <- binomial()$linkinv(eta)
> y <- rbinom(n, 1, mu)
> fit <- cvdglars.fit(X, y, family = binomial)
> coef(fit)
$beta
11 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print -> print -> .local
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/diffeR.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Running examples in 'dimRed-Ex.R' failed
The error most likely occurred in:

> ### Name: NNMF-class
> ### Title: Non-Negative Matrix Factorization
> ### Aliases: NNMF-class NNMF
> 
> ### ** Examples
> 
> dat <- loadDataSet("Iris")
> 
> set.seed(4646)
> factorization <- embed(dat, "NNMF")
Error in chckpkg("NMF") : 
  require 'NMF' package, install it using install.packages('NMF')
Calls: embed ... embed -> .local -> do.call -> <Anonymous> -> chckpkg
Execution halted
Running 'testthat.R' [115s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dimRed)
  Loading required package: DRR
  Loading required package: kernlab
  Loading required package: CVST
  Loading required package: Matrix
  
  Attaching package: 'dimRed'
  
  The following object is masked from 'package:stats':
  
      embed
  
  The following object is masked from 'package:base':
  
      as.data.frame
  
  > 
  > test_check("dimRed", reporter = ListReporter)
  Error: Test failures
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'dimensionality-reduction.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplica
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/discharge.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'bym.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_det
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dissever' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: survival
Error: package or namespace load failed for 'distcomp' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'distr.Rnw' failed with diagnostics:
evaluation nested too deeply: infinite recursion / options(expressions=)?
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'handout.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'diveRsity' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'getting_started_with_dkanr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupli
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.0Mb
Error in re-building vignettes:
  ...
Quitting from lines 597-601 (linest-lsmeans.Rnw) 
Error: processing vignette 'linest-lsmeans.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'docstring' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'documenter.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Running examples in 'document-Ex.R' failed
The error most likely occurred in:

> ### Name: fake_package
> ### Title: Fake a Package From a Single Code File
> ### Aliases: fake_package
> ### Keywords: internal
> 
> ### ** Examples
> 
> document:::fake_package(file_name = system.file("files", "simple.R",
+          package = "document"))
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Introduction_to_document.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplica
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dodgr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'Introduction-to-doremi.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicate
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'dosresmeta.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'compatibility.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dr4pl' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Running examples in 'DRaWR-Ex.R' failed
The error most likely occurred in:

> ### Name: threeCol2MaxMat
> ### Title: threeCol2MaxMat
> ### Aliases: threeCol2MaxMat
> ### Keywords: matrix sparce
> 
> ### ** Examples
> 
> threeCol2MaxMat(a = c("a","b","c","c"), b = c("a","b","b","b"), v = c(1,2,3,4))
3 x 2 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'driftR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'drtmle' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'duawranglr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.6Mb
    libs   5.0Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dynRB' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'dynutils' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'easypackages-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc
Execution halted
Found the following significant warnings:
  Warning: subclass "summaryMpfr" of class "mpfr" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See 'd:/Rcompile/CRANpkg/local/3.4/ecd.Rcheck/00install.out' for details.
Running examples in 'echarts4r-Ex.R' failed
The error most likely occurred in:

> ### Name: e_tree
> ### Title: Tree
> ### Aliases: e_tree e_tree_
> 
> ### ** Examples
> 
> df <- data.frame(
+   parent = c("earth","earth","forest","forest","ocean","ocean","ocean","ocean"), 
+   child = c("ocean","forest","tree","sasquatch","fish","seaweed","mantis shrimp","sea monster")
+ )
> 
> df %>% 
+   e_charts() %>% 
+   e_tree(parent, child)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running examples in 'eclust-Ex.R' failed
The error most likely occurred in:

> ### Name: r_cluster_data
> ### Title: Cluster data using environmental exposure
> ### Aliases: r_cluster_data
> 
> ### ** Examples
> 
> data("tcgaov")
> tcgaov[1:5,1:6, with = FALSE]
             rn subtype E status   OS    ABCA8
1: TCGA-04-1331       4 1      1 1336 3.684824
2: TCGA-04-1332       1 0      1 1247 7.892982
3: TCGA-04-1335       3 1      1   55 5.193188
4: TCGA-04-1336       3 1      0 1495 3.055437
5: TCGA-04-1337       1 0      1   61 3.149427
> Y <- log(tcgaov[["OS"]])
> E <- tcgaov[["E"]]
> genes <- as.matrix(tcgaov[,-c("OS","rn","subtype","E","status"),with = FALSE])
> trainIndex <- drop(caret::createDataPartition(Y, p = 0.5, list = FALSE, times = 1))
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: drop ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Barro_Colorado.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EcoNetGen.Rcheck/00install.out' for details.
Running examples in 'econullnetr-Ex.R' failed
The error most likely occurred in:

> ### Name: generate_edgelist
> ### Title: Export null modelling results
> ### Aliases: generate_edgelist
> 
> ### ** Examples
> 
> set.seed(1234)
> bs.null <- generate_null_net(Broadstone, Broadstone.prey, data.type = "counts",
+                              sims = 10, r.weights = Broadstone.fl)
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
> BS.export <- generate_edgelist(bs.null, signif.level = 0.95)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: generate_edgelist ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'econullnetr-intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'ecospace.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'edeaR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EEM.Rcheck/00install.out' for details.
Running examples in 'eemR-Ex.R' failed
The error most likely occurred in:

> ### Name: eem_bind
> ### Title: Bind eem or eemlist
> ### Aliases: eem_bind
> 
> ### ** Examples
> 
> file <- system.file("extdata/cary/scans_day_1/", "sample1.csv", package = "eemR")
> eem <- eem_read(file)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_g
Calls: eem_read ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
effectFusion: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Error in re-building vignettes:
  ...
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_de
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'elasticIsing' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'elastic_intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'elementR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'emdi' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupli
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'emuR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupli
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'enpls' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EnvStats.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'epidata' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_du
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'epiflows-class.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'defs-and-eqns.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Running examples in 'episode-Ex.R' failed
The error most likely occurred in:

> ### Name: aim
> ### Title: Adaptive Integral Matching (AIM)
> ### Aliases: aim
> 
> ### ** Examples
> 
> set.seed(123)
> # Michaelis-Menten system with two 0-rate reactions
> A <- matrix(c(1, 1, 0, 0,
+   0, 0, 1, 0,
+   0, 0, 1, 0,
+   0, 0, 1, 1,
+   0, 0, 1, 1), ncol = 4, byrow = TRUE)
> B <- matrix(c(0, 0, 1, 0,
+   1, 1, 0, 0,
+   1, 0, 0, 1,
+   0, 1, 0, 0,
+   1, 0, 0, 1), ncol = 4, byrow = TRUE)
> k <- c(0.1, 1.25, 0.5, 0, 0); x0 <- c(E = 5, S = 5, ES = 1.5, P = 1.5)
> Time <- seq(0, 10, by = 1)
> 
> # Simulate data, in second context the catalytic rate has been inhibited
> contexts <- cbind(1, c(1, 1, 0, 1, 1))
> m <- mak(A, B, r = reg(contexts = contexts))
> y <- numsolve(m, c(Time, Time), cbind(x0, x0 + c(2, -2, 0, 0)), contexts * k)
> y[, -1] <- y[, -1] + matrix(rnorm(prod(dim(y[, -1])), sd = .25), nrow = nrow(y))
> 
> # Create optimisation object via data
> o <- opt(y, nlambda = 10)
> 
> # Fit data using Adaptive Integral Matching on mak-object
> a <- aim(m, o)
> a$params$rate
5 x 10 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'episode.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'epubr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'esc' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplic
Execution halted
Error in re-building vignettes:
  ...
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Warning: ALV.DE contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: CS.PA contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: ELE.PA download failed; trying again.
Quitting from lines 56-64 (estudy2-intro.Rmd) 
Error: processing vignette 'estudy2-intro.Rmd' failed with diagnostics:
ELE.PA download failed after two attempts. Error message:
HTTP error 404.
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Error: package or namespace load failed for 'etl' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplic
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'evergreenreviewgraphs.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'eurostat' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'evaluator' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EValue.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Loading required package: plyr
Error: package or namespace load failed for 'evolqg' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dup
Execution halted
** DONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/exampletestr.Rcheck/00install.out' for details.
Running examples in 'expandFunctions-Ex.R' failed
The error most likely occurred in:

> ### Name: coefPlot
> ### Title: Plots coefficients in an impulse response format
> ### Aliases: coefPlot
> 
> ### ** Examples
> 
> set.seed(1)
> nObs <- 100
> X <- distMat(nObs,6)
> A <- cbind(c(1,0,-1,rep(0,3))) # Y will only depend on X[,1] and X[,3]
> Y <- X %*% A + 0.1*rnorm(nObs)
> lassoObj <- easyLASSO(X,Y)
> Yhat <- predict(lassoObj,newx=X)
> yyHatPlot(Y,Yhat)
> coef( lassoObj ) # Sparse coefficients
7 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'expm-Ex.R' failed
The error most likely occurred in:

> ### Name: expAtv
> ### Title: Compute Matrix Exponential exp(A t) * v directly
> ### Aliases: expAtv expmv
> ### Keywords: algebra math
> 
> ### ** Examples
> 
> source(system.file("demo", "exact-fn.R", package = "expm"))
> ##-> rnilMat() ; xct10
> set.seed(1)
> (s5 <- Matrix(m5 <- rnilMat(5))); v <- c(1,6:9)
5 x 5 sparse Matrix of class "dtCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'expss' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'eyelinker' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'ezpickr_vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any,
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'facerec' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_du
Execution halted
Running examples in 'facilitation-Ex.R' failed
The error most likely occurred in:

> ### Name: mat.model
> ### Title: matrix population model
> ### Aliases: mat.model
> 
> ### ** Examples
> 
> # example 1
> mat.model(create.parameters(n=4))
         [,1]      [,2]       [,3]      [,4]
[1,] 0.968036  3.145570  0.3089314  1.029873
[2,] 1.008410 -6.352568  0.0000000  0.000000
[3,] 0.000000  4.491948 -7.5876432  0.000000
[4,] 0.000000  0.000000  4.7233763 -4.541039
> 
> # example 2 
> data(malthusian)
> mat.model(malthusian)
     [,1] [,2] [,3]
[1,]   -6    0 10.0
[2,]    1   -2  0.0
[3,]    0    1 -0.5
> 
> # example 3
> data(twospecies)
> mat.model(twospecies,combine.matrices=TRUE)
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
'LinkingTo' field is unused: package has no 'src' directory
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'farff' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_dupl
Execution halted
** DONE
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'fdrDiscreteNull' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_sub_all<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated,
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'fivethirtyeight-Ex.R'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/forecast.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.1Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
Running examples in 'gcdnet-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.cv.gcdnet
> ### Title: get coefficients or make coefficient predictions from a
> ###   "cv.gcdnet" object.
> ### Aliases: coef.cv.gcdnet
> ### Keywords: models regression
> 
> ### ** Examples
> 
> data(FHT)
> set.seed(2011)
> cv=cv.gcdnet(FHT$x, FHT$y, 
+ 	lambda2 = 1,nfolds=5)
> coef(cv,s="lambda.min")
101 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'gdistance-Ex.R' failed
The error most likely occurred in:

> ### Name: Transition* methods
> ### Title: Extracting and replacing: class Transition
> ### Aliases: [,TransitionLayer,numeric,numeric,missing-method
> ###   [,TransitionLayer,matrix,missing,missing-method
> ###   [<-,TransitionLayer,matrix,missing,ANY-method
> ###   [<-,TransitionLayer,numeric,numeric,ANY-method
> ###   [[,TransitionStack,numeric,missing-method
> ###   [[<-,TransitionStack,numeric,missing,TransitionData-method
> ### Keywords: methods
> 
> ### ** Examples
> 
>   #Create a new raster and set all its values to unity.
>   r <- raster(nrows=18, ncols=36) 
>   r <- setValues(r,rep(1,ncell(r)))
> 
>   #Create TransitionLayer objects
>   tr1 <- transition(r,mean,4)
>   tr2 <- tr1
> 
>   #Extracting and replacing
>   tr1[cbind(1:9,1:9)] <- tr2[cbind(1:9,1:9)]
>   tr1[1:9,1:9] <- tr2[1:9,1:9]
>   tr1[1:5,1:5]
5 x 5 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: 'gdistance'

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

    normalize

Error: processing vignette 'gdistance1.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GeneralizedUmatrix.Rcheck/00install.out' for details.
S3 methods shown with full name in documentation object 'diseq':
  'diseq.ci'

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:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/genlogis.Rcheck/00install.out' for details.
Running examples in 'geostatsp-Ex.R' failed
The error most likely occurred in:

> ### Name: swissRainR
> ### Title: Raster of Swiss rain data
> ### Aliases: swissRainR swissNN
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library('raster')
> ##D border = raster::getData('GADM',country='CHE',level=0)
> ##D 
> ##D myextent = extent(5 ,12,45,49)
> ##D 
> ##D theres=10
> ##D rain = raster::getData('worldclim', var='prec',
> ##D 	res=theres,mask=FALSE)#,lon=20,lat=47)
> ##D rain = raster::crop(rain,myextent)
> ##D plot(rain[['prec3']])
> ##D plot(border,add=TRUE)
> ##D 
> ##D alt = raster::getData('worldclim', var='alt',res=theres)
> ##D alt = raster::crop(alt,extent(rain))
> ##D plot(alt)
> ##D plot(border,add=TRUE)
> ##D 
> ##D 
> ##D bio = raster::getData('worldclim', var='bio',res=theres)
> ##D bio = raster::crop(bio,extent(rain))
> ##D plot(alt)
> ##D plot(border,add=TRUE)
> ##D 
> ##D swissRainR = rain
> ##D #	rain[[c('prec2','prec7')]]
> ##D swissRainR = addLayer(swissRainR,alt)	
> ##D 
> ##D library('geostatsp')
> ##D swissNN = NNmat(swissRainR)
> ##D 	
> ##D save(swissRainR, swissNN,file=
> ##D "/home/patrick/workspace/diseasemapping/pkg/gmrf/data/swissRainR.RData",
> ##D compress='xz'	)	
> ##D 
> ## End(Not run)
> data('swissRainR')
> plot(swissRainR[['prec7']])
> 
> plot(swissRainR[['alt']])
> 
> swissNN[1:4,1:5]
4 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/gfcanalysis.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GGally.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggdendro.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggfittext.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggiraph.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggplot2.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggridges.Rcheck/00install.out' for details.
Package required but not available: 'broom.mixed'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ggthemes.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gifti)
  > 
  > test_check("gifti")
  trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  -- 1. Error: reading gifti files (@test-reader.R#3)  ---------------------------
  cannot open URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  1: download_gifti_data(tdir) at testthat/test-reader.R:3
  2: download.file(url = url, destfile = destfile)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: reading gifti files (@test-reader.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GJRM.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.2Mb
Running examples in 'glmnet-Ex.R' failed
The error most likely occurred in:

> ### Name: cv.glmnet
> ### Title: Cross-validation for glmnet
> ### Aliases: cv.glmnet
> ### 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)
> set.seed(1011)
> cvob1=cv.glmnet(x,y)
> plot(cvob1)
> coef(cvob1)
101 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 115-116 (glmnet_beta.Rmd) 
Error: processing vignette 'glmnet_beta.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Predict: possible error in diag(Nug_opt, m, m, names = FALSE): unused
  argument (names = FALSE)
Running examples in 'GPM-Ex.R' failed
The error most likely occurred in:

> ### Name: Fit
> ### Title: The Fitting Function of 'GPM' Package
> ### Aliases: Fit
> 
> ### ** Examples
> 
> # 1D example: Fit a model (with default settings) and evaluate the performance
> # by computing the root mean squared error (RMSE) in prediction.
> library(lhs)
> library(Rcpp)
> library(RcppArmadillo)
> X <- 5*maximinLHS(9, 1)
> Y <- 2*sin(2*X) + log(X+1)
> M <- Fit(X, Y)
> XF <- matrix(seq(0, 5, length.out = 100), 100, 1)
> YF <- Predict(XF, M)
> RMSE <- sqrt(mean((YF$YF - (2*sin(2*XF) + log(XF+1)))^2))
> 
> # 1D example: Fit a model, evaluate the performance, and plot the response
> # along with 95% prediction interval
> X <- 10*maximinLHS(18, 1) - 5
> Y <- X*cos(X)
> M <- Fit(X, Y)
> XF <- matrix(seq(-5, 5, length.out = 50), 50, 1)
> YF <- Predict(XF, M)
> RMSE <- sqrt(mean((YF$YF - (XF*cos(XF)))^2))
> Draw(M, 1, res = 15)
Error in diag(Nug_opt, m, m, names = FALSE) : 
  unused argument (names = FALSE)
Calls: Draw -> Predict
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R   6.9Mb
Running examples in 'grainchanger-Ex.R' failed
The error most likely occurred in:

> ### Name: nomove_agg
> ### Title: Direct data aggregation
> ### Aliases: nomove_agg
> ### Keywords: aggregate spatial,
> 
> ### ** Examples
> 
> # load required data
> data(g_sf)
> data(cont_ls)
> data(cat_ls)
> 
> # aggregate using mean
> d = nomove_agg(g_sf, cont_ls, "mean")
Error in methods::validObject(y) : invalid class "Extent" object: TRUE
Calls: nomove_agg ... values.list -> value -> value.Future -> resignalConditions
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 39-51 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
invalid class "Extent" object: TRUE
Execution halted
Package suggested but not available for checking: 'taxstats1516'
Running examples in 'gRbase-Ex.R' failed
The error most likely occurred in:

> ### Name: graph-create
> ### Title: Create undirected and directed graphs
> ### Aliases: dag dagList dagList2dgCMatrix dagList2matrix graph-create ug
> ###   ugList ugList2dgCMatrix ugList2matrix
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> ## The following specifications of undirected graphs are equivalent:
> uG1 <- ug(~ a:b:c + c:d)
> uG2 <- ug(c("a","b","c"), c("c","d"))
> uG3 <- ug(c("a","b"), c("a","c"), c("b","c"), c("c","d"))
> 
> graph::edges(uG1)
$a
[1] "b" "c"

$b
[1] "c" "a"

$c
[1] "d" "a" "b"

$d
[1] "c"

> graph::nodes(uG1)
[1] "a" "b" "c" "d"
> 
> ## The following specifications of directed acyclig graphs are equivalent:
> daG1 <- dag(~ a:b:c + b:c + c:d)
> daG2 <- dag(c("a","b","c"), c("b","c"), c("c","d"))
> 
> graph::edges(daG1)
$a
character(0)

$b
[1] "a"

$c
[1] "a" "b"

$d
[1] "c"

> graph::nodes(daG2)
[1] "a" "b" "c" "d"
> 
> ## dag() allows to specify directed graphs with cycles:
> daG4 <- dag(~ a:b + b:c + c:a) # A directed graph but with cycles
> ## A check for acyclicity can be done with
> ## daG5 <- dag(~ a:b + b:c + c:a, forceCheck=TRUE) 
> 
> ## A check for acyclicity is provided by topoSort
> topoSort( daG2 )
[1] "d" "c" "b" "a"
> topoSort( daG4 )
character(0)
> 
> ## Different representations
> uG6 <- ug(~a:b:c + c:d, result="graphNEL")  # default
> uG6
A graphNEL graph with undirected edges
Number of Nodes = 4 
Number of Edges = 4 
> uG7 <- ug(~a:b:c + c:d, result="NEL")       # same
> uG7
A graphNEL graph with undirected edges
Number of Nodes = 4 
Number of Edges = 4 
> uG8 <- ug(~a:b:c + c:d, result="matrix")    # dense matrix
> uG8
  a b c d
a 0 1 1 0
b 1 0 1 0
c 1 1 0 1
d 0 0 1 0
> uG9 <- ug(~a:b:c + c:d, result="dgCMatrix") # sparse matrix
> uG9
4 x 4 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 458-459 (gRbase-graphs.Rnw) 
Error: processing vignette 'gRbase-graphs.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Packages required but not available:
  'EnsDb.Hsapiens.v86' 'EnsDb.Mmusculus.v79' 'org.Rn.eg.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-34\unhbox\voidb@x \penalty \@M \ {}1.
4/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is 124.7Mb
  sub-directories of 1Mb or more:
    java  123.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: caching in reap with long sample (@test-caching.R#76)  ----------
  all(t2[1] <= t1[1]) isn't true.
  
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 5 FAILED: 1
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Package required but not available: 'mlergm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Quitting from lines 189-191 (how-to-make-heuristic.Rmd) 
Error: processing vignette 'how-to-make-heuristic.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/HMP.Rcheck/00install.out' for details.
Missing link or links in documentation object 'profile.nlreg.Rd':
  '[nlreg]{allProfiles.nlreg}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hrbrthemes.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/htmlwidgets.Rcheck/00install.out' for details.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data  12.0Mb
    doc    2.2Mb
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  -- 1. Error: (unknown) (@test-hurdat.R#4)  -------------------------------------
  Timeout was reached: Connection timed out after 10639 milliseconds
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip, skip_empty_rows = skip_empty_rows)
  7: datasource_connection(file, skip, skip_empty_rows, comment)
  8: read_connection(path)
  9: open(con, "rb")
  10: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In for (i in seq_along(cenv$extra)) { :
    closing unused connection 3 (http://www.aoml.noaa.gov/hrd/hurdat/hurdat2.html)
  Execution halted
Running 'testthat.R' [85s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(huxtable)
  > 
  > 
  > we_are_in_R_CMD_check <- TRUE
  > test_check("huxtable")
  -- 1. Failure: Data written in appropriate format (@test-openxlsx.R#101)  ------
  `openxlsx::saveWorkbook(wb, file = "test-xlsx.xlsx", overwrite = TRUE)` produced messages.
  
  == testthat results  ===========================================================
  OK: 888 SKIPPED: 58 FAILED: 1
  1. Failure: Data written in appropriate format (@test-openxlsx.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hyfo.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  13.8Mb
installed size is 23.9Mb
  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  10.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/inlabru.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/IPtoCountry.Rcheck/00install.out' for details.
Running examples in 'irregulAR1-Ex.R' failed
The error most likely occurred in:

> ### Name: ar1_prec_chol_irregular
> ### Title: Upper Cholesky triangle of the precision matrix of a stationary
> ###   Gaussian AR(1) process, observed at irregularly spaced time points.
> ### Aliases: ar1_prec_chol_irregular
> 
> ### ** Examples
> 
> library(Matrix)
> times <- c(1, 4:5, 7)
> rho <- 0.5
> sigma <- 1
> ar1_prec_chol_irregular(times, rho, sigma)
4 x 4 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/jcext.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '.DollarNames.Message', '.DollarNames.Descriptor', '.DollarNames.EnumDescriptor', '.DollarNames.EnumValueDescriptor', '.DollarNames.FileDescriptor', '.DollarNames.FieldDescriptor', '.DollarNames.ServiceDescriptor', '.DollarNames.MethodDescriptor', '.DollarNames.ZeroCopyInputStream', '.DollarNames.ZeroCopyOutputStream', 'with.Message', 'within.Message', 'as.list.Message', 'as.list.Descriptor', 'as.list.EnumDescriptor', 'as.list.FileDescriptor', 'as.list.ServiceDescriptor' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/jmvcore.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/jtools.Rcheck/00install.out' for details.
Running examples in 'KATforDCEMRI-Ex.R' failed
The error most likely occurred in:

> ### Name: KAT
> ### Title: Kinetic Analysis Tool for DCE-MRI
> ### Aliases: KAT
> ### Keywords: kinetic DCEMRI
> 
> ### ** Examples
> 
> ## Create temporary directory for example code output files
> temp_dir <- tempdir(check=FALSE)
Error in tempdir(check = FALSE) : unused argument (check = FALSE)
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Error in re-building vignettes:
  ...
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Error: processing vignette 'pedigree.snw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 116-117 (L0Learn-vignette.Rmd) 
Error: processing vignette 'L0Learn-vignette.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running examples in 'lfe-Ex.R' failed
The error most likely occurred in:

> ### Name: makeDmatrix
> ### Title: Make sparse matrix of dummies from factor list
> ### Aliases: makeDmatrix
> 
> ### ** Examples
> 
> 
>   fl <- lapply(1:3, function(i) factor(sample(3,10,replace=TRUE)))
>   fl
[[1]]
 [1] 1 2 2 3 1 3 3 2 2 1
Levels: 1 2 3

[[2]]
 [1] 1 1 3 2 3 2 3 3 2 3
Levels: 1 2 3

[[3]]
 [1] 3 1 2 1 1 2 1 2 3 2
Levels: 1 2 3

>   makeDmatrix(fl, weights=seq(0.1,1,0.1))
10 x 9 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
unshelf: no visible global function definition for '...length'
Undefined global functions or variables:
  ...length
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/lmerTest.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
magcurve: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'magicaxis-Ex.R' failed
The error most likely occurred in:

> ### Name: magcurve
> ### Title: Draw Function Plots
> ### Aliases: magcurve
> ### Keywords: hplot
> 
> ### ** Examples
> 
> magcurve(sin, -2*pi, 2*pi, xname = "t")
Error in isFALSE(add) : could not find function "isFALSE"
Calls: magcurve
Execution halted
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  34.2Mb
Running examples in 'mapfit-Ex.R' failed
The error most likely occurred in:

> ### Name: cf1-class
> ### Title: Class of canonical form 1 (PH distribution)
> ### Aliases: cf1-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## create a CF1 with 5 phases
> (param1 <- cf1(5))
An object of class "cf1"
Slot "rate":
[1] 1 1 1 1 1

Slot "size":
[1] 5

Slot "alpha":
[1] 0.2 0.2 0.2 0.2 0.2

Slot "Q":
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
is_literally_false: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/marmap.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Running examples in 'MatrixModels-Ex.R' failed
The error most likely occurred in:

> ### Name: lm.fit.sparse
> ### Title: Fitter Function for Sparse Linear Models
> ### Aliases: lm.fit.sparse
> ### Keywords: regression array
> 
> ### ** Examples
> 
> dd <- expand.grid(a = as.factor(1:3),
+                   b = as.factor(1:4),
+                   c = as.factor(1:2),
+                   d= as.factor(1:8))
> n <- nrow(dd <- dd[rep(seq_len(nrow(dd)), each = 10), ])
> set.seed(17)
> dM <- cbind(dd, x = round(rnorm(n), 1))
> ## randomly drop some
> n <- nrow(dM <- dM[- sample(n, 50),])
> dM <- within(dM, { A <- c(2,5,10)[a]
+                    B <- c(-10,-1, 3:4)[b]
+                    C <- c(-8,8)[c]
+                    D <- c(10*(-5:-2), 20*c(0, 3:5))[d]
+    Y <- A + B + A*B + C + D + A*D + C*x + rnorm(n)/10
+    wts <- sample(1:10, n, replace=TRUE)
+    rm(A,B,C,D)
+ })
> str(dM) # 1870 x 7
'data.frame':	1870 obs. of  7 variables:
 $ a  : Factor w/ 3 levels "1","2","3": 1 1 1 1 1 1 1 1 1 2 ...
 $ b  : Factor w/ 4 levels "1","2","3","4": 1 1 1 1 1 1 1 1 1 1 ...
 $ c  : Factor w/ 2 levels "1","2": 1 1 1 1 1 1 1 1 1 1 ...
 $ d  : Factor w/ 8 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
 $ x  : num  -1 -0.1 -0.2 -0.8 0.8 -0.2 1 0.3 0.4 1.2 ...
 $ wts: int  7 6 3 4 6 10 3 10 3 2 ...
 $ Y  : num  -178 -185 -185 -180 -192 ...
> 
> X <- Matrix::sparse.model.matrix( ~ (a+b+c+d)^2 + c*x, data = dM)
> dim(X) # 1870 x 69
[1] 1870   69
> X[1:10, 1:20]
10 x 20 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
printSpMatrix2: no visible global function definition for 'isFALSE'
print,sparseMatrix: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running 'Class+Meth.R' [3s]
Running the tests in 'tests/Class+Meth.R' failed.
Complete output:
  > library(Matrix)
  > source(system.file("test-tools.R", package = "Matrix"))# identical3(),
  Loading required package: tools
  >                                         # further  checkMatrix(), etc
  > if(interactive()) options(error = recover)
  > options(warn=1)# show as they happen
  > cat("doExtras:",doExtras,"\n")
  doExtras: FALSE 
  > 
  > no.Mcl <- function(cl) ## TRUE if MatrixClass() returns empty, i
  +     identical(Matrix:::MatrixClass(cl), character(0))
  > 
  > setClass("myDGC", contains = "dgCMatrix")
  > M <- new("myDGC", as(Matrix(c(-2:4, rep(0,9)), 4), "CsparseMatrix"))
  > M
  4 x 4 sparse Matrix of class "myDGC"
  Error in isFALSE(suppRows) : could not find function "isFALSE"
  Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Design-issues.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running examples in 'Matrix.utils-Ex.R' failed
The error most likely occurred in:

> ### Name: dMcast
> ### Title: Casts or pivots a long 'data frame' into a wide sparse matrix
> ### Aliases: dMcast
> 
> ### ** Examples
> 
> #Classic air quality example
> melt<-function(data,idColumns)
+ {
+   cols<-setdiff(colnames(data),idColumns)
+   results<-lapply(cols,function (x) cbind(data[,idColumns],variable=x,value=as.numeric(data[,x])))
+   results<-Reduce(rbind,results)
+ }
> names(airquality) <- tolower(names(airquality))
> aqm <- melt(airquality, idColumns=c("month", "day"))
> dMcast(aqm, month:day ~variable,fun.aggregate = 'mean',value.var='value')
153 x 4 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Running examples in 'MDPtoolbox-Ex.R' failed
The error most likely occurred in:

> ### Name: MDPtoolbox-package
> ### Title: Markov Decision Processes Toolbox
> ### Aliases: MDPtoolbox-package MDPtoolbox
> 
> ### ** Examples
> 
> # Generates a random MDP problem
> set.seed(0)
> mdp_example_rand(2, 2)
$P
, , 1

          [,1]      [,2]
[1,] 0.7067168 0.2932832
[2,] 0.3166993 0.6833007

, , 2

          [,1]      [,2]
[1,] 0.5027173 0.4972827
[2,] 0.1759329 0.8240671


$R
, , 1

          [,1]       [,2]
[1,] 0.3215956 -0.8764275
[2,] 0.2582281 -0.5880509

, , 2

           [,1]       [,2]
[1,] -0.6468865 -0.2317926
[2,]  0.3740457  0.5396828


> mdp_example_rand(2, 2, FALSE)
$P
, , 1

          [,1]      [,2]
[1,] 0.3341148 0.6658852
[2,] 0.6537750 0.3462250

, , 2

          [,1]      [,2]
[1,] 0.7856254 0.2143746
[2,] 0.5892068 0.4107932


$R
, , 1

           [,1]       [,2]
[1,] -0.7488898 -0.2277718
[2,] -0.4655587 -0.9732193

, , 2

           [,1]        [,2]
[1,] -0.2352241 -0.31930201
[2,]  0.7393817 -0.03583977


> mdp_example_rand(2, 2, TRUE)
Warning in `[<-`(`*tmp*`, a, value = <S4 object of class "dgCMatrix">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, a, value = <S4 object of class "dgCMatrix">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, a, value = <S4 object of class "dgeMatrix">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, a, value = <S4 object of class "dgeMatrix">) :
  implicit list embedding of S4 objects is deprecated
$P
$P[[1]]
2 x 2 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print -> print -> .local
Execution halted
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

Loading required package: lattice
Error: package or namespace load failed for 'mdsr':
 .onAttach failed in attachNamespace() for 'mdsr', details:
  call: value[[3L]](cond)
  error: Package 'lattice' version 0.20.38 cannot be unloaded:
 Error in unloadNamespace(package) : namespace 'lattice' is imported by 'nlme', 'Matrix', 'mosaic' so cannot be unloaded
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
Running examples in 'mefa4-Ex.R' failed
The error most likely occurred in:

> ### Name: Mefa
> ### Title: 'Mefa' Class
> ### Aliases: Mefa Mefa-class MefaDataFrame MefaMatrix mefa stcs
> ###   MefaDataFrame-class MefaMatrix-class mefa-class stcs-class
> ###   dim,Mefa-method dimnames,Mefa-method dimnames<-,Mefa,list-method
> ###   t,Mefa-method show,Mefa-method stack,Mefa-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> x <- data.frame(
+     sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
+     species = c(paste("Species", c(1,1,1,2,3), sep="."),  "zero.pseudo"),
+     count = c(1,2,10,3,4,0))
> samp <- data.frame(samples=levels(x$sample), var1=1:2)
> taxa <- data.frame(specnames=levels(x$species), var2=c("b","a"))
> rownames(samp) <- samp$samples
> rownames(taxa) <- taxa$specnames
> 
> ## Xtab class, counts by repetitions in RHS
> (x0 <- Xtab(~ sample + species, x))
4 x 4 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 method 'format.SQLiteConnection' was declared in NAMESPACE but not found
  Warning: namespace 'topGO' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.4/metaboGSE.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Error in re-building vignettes:
  ...
Error in highr::hi_andre(x, options$engine, format) : 
  please first install highlight from http://www.andre-simon.de
Error in highr::hi_andre(x, options$engine, format) : 
  please first install highlight from http://www.andre-simon.de
Quitting from lines 182-190 (guide.Rnw) 
Error: processing vignette 'guide.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
estim: no visible global function definition for 'var'
metareg: no visible global function definition for 'pchisq'
metareg: no visible global function definition for 'pnorm'
metareg: no visible global function definition for 'pt'
metatest: no visible global function definition for 'model.matrix'
metatest: no visible global function definition for 'model.response'
permute: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  model.matrix model.response pchisq pnorm pt rbinom var
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pchisq",
             "pnorm", "pt", "rbinom", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/micromap.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/mlr.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: basefun
Loading required package: variables
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/

Attaching package: 'flexsurv'

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

    Hgompertz, Hllogis, Hlnorm, Hweibull, dgompertz, dllogis,
    hgompertz, hllogis, hlnorm, hweibull, pgompertz, pllogis,
    qgompertz, qllogis, rgompertz, rllogis


Attaching package: 'grid'

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

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

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

    geyser

trying URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Content type 'application/octet-stream' length 2292581 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health

warning: solve(): system seems singular; attempting approx solution
Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health
Warning: contrasts dropped from factor R_health
Quitting from lines 1532-1539 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running examples in 'mltools-Ex.R' failed
The error most likely occurred in:

> ### Name: sparsify
> ### Title: Sparsify
> ### Aliases: sparsify
> 
> ### ** Examples
> 
> library(data.table)
> library(Matrix)
> 
> dt <- data.table(
+   intCol=c(1L, NA_integer_, 3L, 0L),
+   realCol=c(NA, 2, NA, NA),
+   logCol=c(TRUE, FALSE, TRUE, FALSE),
+   ofCol=factor(c("a", "b", NA, "b"), levels=c("a", "b", "c"), ordered=TRUE),
+   ufCol=factor(c("a", NA, "c", "b"), ordered=FALSE)
+ )
> 
> sparsify(dt)
4 x 7 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'mmmgee-Ex.R' failed
The error most likely occurred in:

> ### Name: mmmgee
> ### Title: Covariance Matrix Estimation for Multiple Marginal GEE Models
> ### Aliases: mmmgee
> 
> ### ** Examples
> 
> data(keratosis)
> m1<-geem2(clearance~trt,id=id,data=keratosis,family=binomial,corstr="independence")
> m2<-geem2(pain~trt,id=id,data=keratosis[keratosis$lesion==1,],family=gaussian,corstr="independence")
> mmmgee(x=list(m1,m2),biascorr=TRUE)
$beta
(Intercept)        trtB        trtC        trtD (Intercept)        trtB 
 0.71195651  0.07650085 -0.27164467 -1.06559655  5.75333333 -1.04000000 
       trtC        trtD 
-1.13833333 -1.99166667 

$V
8 x 8 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   1.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Running examples in 'msgl-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.msgl
> ### Title: Nonzero coefficients
> ### Aliases: coef.msgl
> 
> ### ** Examples
> 
> data(SimData)
> 
> 
> lambda <- msgl::lambda(x, classes, alpha = .5, d = 50, lambda.min = 0.05)
> fit <- msgl::fit(x, classes, alpha = .5, lambda = lambda)

Running msgl (dense design matrix) 

 Samples:  Features:  Classes:  Groups:  Parameters: 
       100        401        10      401        4.01k

0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> 
> # the nonzero coefficients of the models 1, 10 and 20
> coef(fit, index = c(1,10,20))
[[1]]
10 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print -> print -> .local
Execution halted
Error in re-building vignettes:
  ...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 98-99 (msgl-getting-started.Rmd) 
Error: processing vignette 'msgl-getting-started.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.4/msgps.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'mvtnorm'

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

> ### Name: matrixFDM
> ### Title: Finite Difference Matrix Generator
> ### Aliases: matrixFDM
> 
> ### ** Examples
> 
> # finite difference matrix for uniformly-spaced two-asset option
> require("Matrix")
> S1 <- list(seq(0, 5, by=1), seq(0, 5, by=1))
> rf <- 0.1
> q <- c(0.05, 0.04)
> vol <- c(0.20, 0.25)
> rho <- matrix(c(1,-0.5,-0.5,1), 2, 2)
> matrixFDM(S1, rf, q, vol, rho)
36 x 36 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MXM.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
Running examples in 'nadiv-Ex.R' failed
The error most likely occurred in:

> ### Name: makeA
> ### Title: Creates the additive genetic relationship matrix
> ### Aliases: makeA
> 
> ### ** Examples
> 
> 
>  makeA(Mrode2)
6 x 6 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Error in re-building vignettes:
  ...
Quitting from lines 146-148 (neat.Rmd) 
Error: processing vignette 'neat.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
Running examples in 'netregR-Ex.R' failed
The error most likely occurred in:

> ### Name: build_exchangeable_matrix
> ### Title: Build an exchangeable matrix of sparseMatrix class
> ### Aliases: build_exchangeable_matrix
> ### Keywords: external
> 
> ### ** Examples
> 
> n <- 5
> build_exchangeable_matrix(n, rphi(n, seed=1))
20 x 20 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'networkR-Ex.R' failed
The error most likely occurred in:

> ### Name: adjacency
> ### Title: Create adjacency matrix
> ### Aliases: adjacency
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> from <- c("A", "A", "A", "B", "C")
> to <- c("B", "C", "D", "D", "E")
> adjacency(from, to)
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         4.0Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.5Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/NMF.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'OmnibusFisher-Ex.R'
Running examples in 'ompr-Ex.R' failed
The error most likely occurred in:

> ### Name: extract_constraints
> ### Title: Extract the constraint matrix, the right hand side and the sense
> ###   from a model
> ### Aliases: extract_constraints
> 
> ### ** Examples
> 
> library(magrittr)
> model <- MIPModel() %>%
+   add_variable(x[i], i = 1:3) %>%
+   add_variable(y[i], i = 1:3) %>%
+   add_constraint(x[i] + y[i] <= 1, i = 1:3)
> extract_constraints(model)
$matrix
3 x 6 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/OOBCurve.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/OpasnetUtils.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/OpenML.Rcheck/00install.out' for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     6.7Mb
    models   4.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/OpenStreetMap.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/OSMscale.Rcheck/00install.out' for details.
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'overture-Ex.R'
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("pacman")
  > options(repos="http://cran.rstudio.com/")
  > 
  > 
  > test_check("pacman")
  -- 1. Error: p_install_gh works (@test-p_install_gh.R#5)  ----------------------
  HTTP error 404.
    Not Found
  
    Rate limit remaining: 59/60
    Rate limit reset at: 2018-10-22 00:51:57 UTC
  
    
  1: expect_false(p_install_gh("greg/iDontExistAnywhere")) at testthat/test-p_install_gh.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: p_install_gh("greg/iDontExistAnywhere")
  5: lapply(package, function(x) {
         devtools::install_github(x, dependencies = dependencies, ...)
     })
  6: FUN(X[[i]], ...)
  7: devtools::install_github(x, dependencies = dependencies, ...)
  8: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, 
         upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, 
         repos = repos, type = type, ...)
  9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
  10: FUN(X[[i]], ...)
  11: remote_package_name(remote)
  12: remote_package_name.github_remote(remote)
  13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, 
         host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), 
         use_curl = use_curl)
  
  == testthat results  ===========================================================
  OK: 54 SKIPPED: 3 FAILED: 1
  1. Error: p_install_gh works (@test-p_install_gh.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'pact_vignette.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/PairedData.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/paleofire.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...


Error: processing vignette 'PANDA.Rnw' failed with diagnostics:
 chunk 6 
Error in initialize(value, ...) : 
  argument "go_id" is missing, with no default
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.3Mb
    extdata   9.5Mb
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
Error in re-building vignettes:
  ...
Loading required package: pbkrtest
Loading required package: lme4
Loading required package: Matrix
refitting model(s) with ML (instead of REML)
refitting model(s) with ML (instead of REML)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00308812 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0027166 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00298539 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00343782 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.0030478 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00355907 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00267549 (tol = 0.002, component 1)
Error: processing vignette 'pbkrtest-introduction.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  12.0Mb
Running examples in 'pedigreemm-Ex.R' failed
The error most likely occurred in:

> ### Name: getA
> ### Title: Additive Relationship Matrix
> ### Aliases: getA
> ### Keywords: array algebra
> 
> ### ** Examples
> 
> 
> ## Example from chapter 2 of Mrode (2005)
> 
> ped <- pedigree(sire = c(NA,NA,1, 1,4,5),
+                 dam  = c(NA,NA,2,NA,3,2), label= 1:6)
> (getA(ped))
6 x 6 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'pedigreeTools-Ex.R' failed
The error most likely occurred in:

> ### Name: getA
> ### Title: Additive Relationship Matrix
> ### Aliases: getA
> ### Keywords: array
> 
> ### ** Examples
> 
> ped <- pedigree(sire=c(NA,NA,1,1,4,5), dam=c(NA,NA,2,NA,3,2), label=1:6)
> getA(ped)
6 x 6 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/PhaseType.Rcheck/00install.out' for details.
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  Loading required package: bitops
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Error in download.file(url, destfile = tmp, mode = "w") : 
    cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  -- 1. Error: (unknown) (@testphenocamapi.R#11)  --------------------------------
  file was not found on the server!
  1: get_pheno_ts(site = "dukehw", vegType = "DB", roiID = 1000, type = "3day") at testthat/testphenocamapi.R:11
  2: stop("file was not found on the server!")
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testphenocamapi.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'phyloseqGraphTest-Ex.R' failed
The error most likely occurred in:

> ### Name: graph_perm_test
> ### Title: Performs graph-based permutation tests
> ### Aliases: graph_perm_test
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: graph_perm_test ... distance -> do.call -> do.call -> vegdist -> vegdist -> .C
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 128-134 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
"veg_distance" not available for .C() for package "vegan"
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    3.0Mb
pkgverse: possible error in tempdir(check = TRUE): unused argument
  (check = TRUE)
S3 methods shown with full name in documentation object 'rbind.fill':
  'rbind.fill'

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  'rbind.fill.matrix'

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  8.0Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/PReMiuM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/prevR.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
Running examples in 'prioritizr-Ex.R' failed
The error most likely occurred in:

> ### Name: rij_matrix
> ### Title: Feature by planning unit matrix
> ### Aliases: rij_matrix rij_matrix,Raster,Raster-method
> ###   rij_matrix,Spatial,Raster-method rij_matrix rij_matrix
> 
> ### ** Examples
> 
> # load data
> data(sim_pu_raster, sim_pu_polygons, sim_pu_zones_stack)
> 
> # create rij matrix using raster layer planning units
> rij_raster <- rij_matrix(sim_pu_raster, sim_features)
> print(rij_raster)
5 x 90 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print -> print -> .local
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/PRISMA.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: ggplot2
Error: processing vignette 'PRISMA.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/pROC.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      1.6Mb
Running examples in 'proxyC-Ex.R' failed
The error most likely occurred in:

> ### Name: simil
> ### Title: Compute similiarty/distance between raws or columns of large
> ###   matrices
> ### Aliases: simil dist
> 
> ### ** Examples
> 
> mt <- Matrix::rsparsematrix(100, 100, 0.01)
> simil(mt, method = "cosine")[1:5, 1:5]
5 x 5 sparse Matrix of class "dsTMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  > options(testthat.use_colours = FALSE)
  > test_check("psd")
  Loading required package: psd
  Loaded psd (1.0.1) -- Adaptive multitaper spectrum estimation
  -- 1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26)  ----------
  `FFT(x.)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 161 SKIPPED: 0 FAILED: 1
  1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > #
  > # The Hadley-verse is an amazing place: unit testing via testthat
  > # See also  http://r-pkgs.had.co.nz/tests.html
  > #
  > library(testthat)
  > options(testthat.use_colours = FALSE)
  > test_check("psd")
  Loading required package: psd
  Loaded psd (1.0.1) -- Adaptive multitaper spectrum estimation
  -- 1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26)  ----------
  `FFT(x.)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 161 SKIPPED: 0 FAILED: 1
  1. Failure: fftw::FFT expects numeric or complex (@test-fft.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
simulate_data_regression: possible error in diag(x = 1, nrow = n_var +
  1, ncol = n_var + 1, names = TRUE): unused argument (names = TRUE)
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'psycho-Ex.R'
Running examples in 'psycho-Ex.R' failed
The error most likely occurred in:

> ### Name: simulate_data_regression
> ### Title: Simulates data for single or multiple regression.
> ### Aliases: simulate_data_regression
> 
> ### ** Examples
> 
> library(psycho)
> 
> data <- simulate_data_regression(coefs=c(0.1, 0.8), sample=50, error=0)
Error in diag(x = 1, nrow = n_var + 1, ncol = n_var + 1, names = TRUE) : 
  unused argument (names = TRUE)
Calls: simulate_data_regression
Execution halted
Functions or methods with usage in documentation object 'ConspiracistBeliefs2016' but not in code:
  data

Functions or methods with usage in documentation object 'Sim3PL' but not in code:
  data
Undocumented arguments in documentation object 'ConspiracistBeliefs2016'
  'ConspiracistBeliefs2016' 'package'
Objects in \usage without \alias in documentation object 'ConspiracistBeliefs2016':
  'data'

Undocumented arguments in documentation object 'Sim3PL'
  'Sim3PL' 'package'
Objects in \usage without \alias in documentation object 'Sim3PL':
  'data'

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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
Running examples in 'qlcMatrix-Ex.R' failed
The error most likely occurred in:

> ### Name: Array
> ### Title: Sparse Arrays ("Tensors")
> ### Aliases: Array sparseArray as.Matrix
> 
> ### ** Examples
> 
> x <- matrix(c(1, 0, 0, 2), nrow = 2)
> s <- as.simple_triplet_matrix(x)
> str(s)
List of 6
 $ i       : int [1:2] 1 2
 $ j       : int [1:2] 1 2
 $ v       : num [1:2] 1 2
 $ nrow    : int 2
 $ ncol    : int 2
 $ dimnames: NULL
 - attr(*, "class")= chr "simple_triplet_matrix"
> 
> as.Matrix(s)
2 x 2 sparse Matrix of class "dgTMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-33 (transformingDataSparse.Rmd) 
Error: processing vignette 'transformingDataSparse.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.3Mb
Error in re-building vignettes:
  ...
Package version: 1.4.1
Parallel computing: 2 of 32 threads used.
See https://quanteda.io for tutorials and examples.

Attaching package: 'quanteda'

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

    View

Quitting from lines 269-274 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/quickPlot.Rcheck/00install.out' for details.
Running examples in 'qut-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.qut
> ### Title: Make predictions from a "qut" object.
> ### Aliases: predict.qut coef.qut
> 
> ### ** Examples
> 
> 	set.seed(1234)
> 	x=matrix(rnorm(200*20),200,20)
> 	y1=x[,1]*10+rnorm(100)
> 
> 	fit1=qut(y1,x,family=gaussian,sigma=1)
> 	predict(fit1,newx=x[1:5,])
           [,1]
[1,] -11.951276
[2,]   2.838670
[3,]  10.878887
[4,] -23.295406
[5,]   4.350003
> 	predict(fit1,newx=x[1:5,],mode='lasso')
              1
[1,] -11.712122
[2,]   2.768922
[3,]  10.641212
[4,] -22.819320
[5,]   4.248690
> 	y1[1:5]
[1] -13.033531   1.960580  10.649899 -21.540964   4.993016
> 	
> 	coef(fit1,mode='lasso')
21 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Package suggested but not available for checking: 'rcom'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.6Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   3.0Mb
Missing or unexported object: 'base::...elt'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/randstr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/rangeMapper.Rcheck/00install.out' for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RBPcurve.Rcheck/00install.out' for details.
indexplot: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'RcmdrMisc-Ex.R' failed
The error most likely occurred in:

> ### Name: indexplot
> ### Title: Index Plots
> ### Aliases: indexplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require("car")){
+     with(Prestige, indexplot(income, id.n=2, labels=rownames(Prestige)))
+     indexplot(Prestige[, c("income", "education", "prestige")], 
+         groups = Prestige$type, id.n=2)
+ }
Error in isFALSE(legend) : could not find function "isFALSE"
Calls: with -> with.default -> eval -> eval -> indexplot
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RcmdrPlugin.lfstat.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'effects'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: (unknown) (@test_deputados.R#81)  ---------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  -- 2. Error: (unknown) (@test_proposicoes.R#91)  -------------------------------
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  -- 3. Error: (unknown) (@test_votacoes.R#70)  ----------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
    libs      1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in 'RDFTensor-Ex.R' failed
The error most likely occurred in:

> ### Name: Tensor_error
> ### Title: RESCAL Tensor error
> ### Aliases: Tensor_error
> 
> ### ** Examples
> 
>  X1=matrix(c(1,0,0,0,0, 0,1,0,0,0, 0,0,1,1,0, 0,0,0,0,1, 1,0,0,0,0),byrow=TRUE,nrow=5,ncol=5)
>     X2=matrix(c(0,1,0,1,1, 1,0,0,1,0, 0,1,0,1,1, 0,0,0,0,1, 0,0,1,0,0),byrow=TRUE,nrow=5,ncol=5)
>     X2_=matrix(c(0,1,0,1,1, 1,0,0,1,0, 0,0,0,0,0, 0,0,0,0,1, 0,0,1,0,0),byrow=TRUE,nrow=5,ncol=5)
>     X=list(t(X1),t(X2),t(X2_))
> 
>     N=nrow(X1)
>     Xs=list()
>     for(s in 1:length(X)){
+       aa=which(X[[s]]==1,arr.ind=TRUE)
+       Xs[[s]]=Matrix::sparseMatrix(x=rep(1,nrow(aa)),i=aa[,1],j=aa[,2],dims=c(N,N))
+     }
> 
>     print(Xs)
[[1]]
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running 'testthat.R' [18s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rdhs)
  > 
  > Sys.setenv("rdhs_RENVIRON_PERMISSION" = 1)
  > test_check("rdhs")
  -- 1. Error: update_rdhs_config (@test_miscellaneous.R#97)  --------------------
  cannot read workspace version 3 written by R 3.6.0; need R 3.5.0 or newer
  1: dhs_data_updates() at testthat/test_miscellaneous.R:97
  2: handle_api_request(endpoint, query, all_results, client, force)
  3: check_for_client()
  4: rdhs_setup()
  5: client_dhs(config = config, root = config$cache_path)
  6: client_cache_date(root = root)
  7: readRDS(file.path(cache_dir, client_file_name()))
  
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZMR61FL.ZIP&Tp=1&Ctry_Code=zz&survey_id=0&doctype=dhs'
  Content type 'application/x-zip-compressed' length 597481 bytes (583 KB)
  ==================================================
  downloaded 583 KB
  
    adding: temp/RtmpOs0paC/file303dc79bd6887/ZZMR61FL.DAT (deflated 85%)
  trying URL 'https://dhsprogram.com/customcf/legacy/data/sample_download_dataset.cfm?Filename=ZZAR61FL.ZIP&Tp=4&Ctry_Code=zz&survey_id=0&doctype=hiv'
  Content type 'application/x-zip-compressed' length 81939 bytes (80 KB)
  ==================================================
  downloaded 80 KB
  
  == testthat results  ===========================================================
  OK: 30 SKIPPED: 42 FAILED: 1
  1. Error: update_rdhs_config (@test_miscellaneous.R#97) 
  
  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/3.4/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'pkgcond'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.9Mb
Running examples in 'RealVAMS-Ex.R' failed
The error most likely occurred in:

> ### Name: RealVAMS-package
> ### Title: Multivariate VAM Fitting
> ### Aliases: RealVAMS-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(example.score.data)
> data(example.outcome.data)
> #The next line exists to show that the function can run and that the package
> #installed correctly. This is a CRAN requirement to ensure that the package
> #works in future version of R
> RealVAMS(example.score.data,example.outcome.data,max.PQL.it=1,max.iter.EM=2,
+ var.parm.hessian=FALSE)
Beginning EM algorithm
Iteration Time:  2.87  seconds


 End EM Algorithm.


iter: 2 
log-likelihood: -5968.5684066 
change in loglik: 789.9311722 
fixed effects: 49.9994 0.4135 99.8157 0.1226 
R_i:
       [,1]   [,2]    [,3]    [,4]
[1,] 5.1456 1.1888  1.0252  0.0766
[2,] 1.1888 5.6632  1.2798  0.0941
[3,] 1.0252 1.2798  5.6170 -0.0420
[4,] 0.0766 0.0941 -0.0420  1.0000

       [,1]   [,2]    [,3]    [,4]
[1,] 1.0000 0.2202  0.1907  0.0338
[2,] 0.2202 1.0000  0.2269  0.0395
[3,] 0.1907 0.2269  1.0000 -0.0177
[4,] 0.0338 0.0395 -0.0177  1.0000


gamma_teach_year 1 
2 x 2 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: RealVAMS -> vp_cp -> print -> print -> .local
Execution halted
Running examples in 'RealVAMS-Ex.R' failed
The error most likely occurred in:

> ### Name: RealVAMS-package
> ### Title: Multivariate VAM Fitting
> ### Aliases: RealVAMS-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(example.score.data)
> data(example.outcome.data)
> #The next line exists to show that the function can run and that the package
> #installed correctly. This is a CRAN requirement to ensure that the package
> #works in future version of R
> RealVAMS(example.score.data,example.outcome.data,max.PQL.it=1,max.iter.EM=2,
+ var.parm.hessian=FALSE)
Beginning EM algorithm
Iteration Time:  2.95  seconds


 End EM Algorithm.


iter: 2 
log-likelihood: -5968.5684066 
change in loglik: 789.9311722 
fixed effects: 49.9994 0.4135 99.8157 0.1226 
R_i:
       [,1]   [,2]    [,3]    [,4]
[1,] 5.1456 1.1888  1.0252  0.0766
[2,] 1.1888 5.6632  1.2798  0.0941
[3,] 1.0252 1.2798  5.6170 -0.0420
[4,] 0.0766 0.0941 -0.0420  1.0000

       [,1]   [,2]    [,3]    [,4]
[1,] 1.0000 0.2202  0.1907  0.0338
[2,] 0.2202 1.0000  0.2269  0.0395
[3,] 0.1907 0.2269  1.0000 -0.0177
[4,] 0.0338 0.0395 -0.0177  1.0000


gamma_teach_year 1 
2 x 2 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: RealVAMS -> vp_cp -> print -> print -> .local
Execution halted
Running examples in 'recommenderlab-Ex.R' failed
The error most likely occurred in:

> ### Name: sparseNAMatrix-class
> ### Title: Sparse Matrix Representation With NAs Not Explicitly Stored
> ### Aliases: dropNA dropNA2matrix
> 
> ### ** Examples
> 
> m <- matrix(sample(c(NA,0:5),50, replace=TRUE, prob=c(.5,rep(.5/6,6))),
+     nrow=5, ncol=10, dimnames = list(users=paste('u', 1:5, sep=''),
+     items=paste('i', 1:10, sep='')))
> m
     items
users i1 i2 i3 i4 i5 i6 i7 i8 i9 i10
   u1 NA  5 NA NA  0 NA NA  3  4   4
   u2 NA  0 NA  3 NA NA  2  4  2  NA
   u3  1  2  3  0  2 NA NA NA  4  NA
   u4  5  2 NA NA NA  5 NA  3  1   3
   u5 NA NA  4  4 NA NA  4 NA  1   3
> 
> ## drop all NAs in the representation
> sparse <- dropNA(m)
> sparse
5 x 10 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: arules

Attaching package: 'arules'

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

    abbreviate, write

Loading required package: proxy

Attaching package: 'proxy'

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

    as.matrix

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

    as.dist, dist

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

    as.matrix

Loading required package: registry
Error: processing vignette 'recommenderlab.Rnw' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'Repliscope-Ex.R'
S3 methods shown with full name in documentation object 'all.vars.character':
  'all.vars.character'

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.
rec: no visible global function definition for 'isFALSE'
reweight.contingencytable: no visible global function definition for
  'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'revengc-Ex.R' failed
The error most likely occurred in:

> ### Name: rec
> ### Title: Reverse engineering censored and decoupled data
> ### Aliases: rec
> ### Keywords: Poisson negative binomial univariate table frequency table
> ###   count data censored dispersion truncated contingency
> 
> ### ** Examples
> 
>   # provide two averages
>   # seed.matrix defaults to a matrix of ones
>   # seed.estimation.method defaults to ipfp
>   twoaverages.results<-rec(
+      X= 4.4,
+      Y = 571.3,
+      Xlowerbound = 1,
+      Xupperbound = 20,
+      Ylowerbound = 520,
+      Yupperbound = 620)
[1] "Truncated Poisson distributions were calculated for both the X and Y variable (i.e. Var(X) = E(X) and Var(Y) = E(Y) has to be assumed when only averages are provided)"
[1] "The default seed matrix implies independence between variables 1/(length(Xlowerbound:Xupperbound)*length(Ylowerbound:Yupperbound)) (i.e. independence between variables has to be assumed when there is no external information about the joint distribution)"
Error in isFALSE(all.equal(sum(seedfinal), 1)) : 
  could not find function "isFALSE"
Calls: rec
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Rfast.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/rfigshare.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RGraphics.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
Running examples in 'RGtk2Extras-Ex.R' failed
The error most likely occurred in:

> ### Name: gtkDfEditDoTask
> ### Title: Editor change handling.
> ### Aliases: gtkDfEditDoTask
> 
> ### ** Examples
> 
> 
> win = gtkWindowNew("gtkDfEdit Demo")
Error in .RGtkCall("S_gtk_window_new", type, PACKAGE = "RGtk2") : 
  Could not parse enum value gtkDfEdit Demo
Calls: gtkWindowNew -> .RGtkCall -> .Call
Execution halted
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RIdeogram.Rcheck/00install.out' for details.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/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/3.4/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.4/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  8.6Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Packages required and available but unsuitable versions:
  'impute' 'MassSpecWavelet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'hgu95av2cdf' 'illuminaHumanv3.db'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
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/3.4/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/3.4/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/3.4/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 19.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/rWBclimate.Rcheck/00install.out' for details.
Running examples in 'rWind-Ex.R' failed
The error most likely occurred in:

> ### Name: cost.FMGS
> ### Title: Compute flow-based cost or conductance
> ### Aliases: cost.FMGS flow.dispersion
> ### Keywords: ~anisotropy ~conductance
> 
> ### ** Examples
> 
> 
> require(gdistance)
Loading required package: gdistance
Loading required package: raster
Loading required package: sp
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    decompose, spectrum

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

    union

Loading required package: Matrix

Attaching package: 'gdistance'

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

    normalize

> 
> data(wind.data)
> 
> wind <- wind2raster(wind.data)
> 
> Conductance<-flow.dispersion(wind, type="passive")
> 
> transitionMatrix(Conductance)
651 x 651 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
Error in re-building vignettes:
  ...
Quitting from lines 93-118 (ssm-matrix.Rmd) 
Error: processing vignette 'ssm-matrix.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
hier_convert : .to_df: no visible global function definition for
  'isFALSE'
Undefined global functions or variables:
  isFALSE
Error in re-building vignettes:
  ...
Quitting from lines 95-98 (usage.Rmd) 
Error: processing vignette 'usage.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running examples in 'sdcTable-Ex.R' failed
The error most likely occurred in:

> ### Name: makeProblem
> ### Title: create 'sdcProblem-class'-objects
> ### Aliases: makeProblem
> 
> ### ** Examples
> 
> # loading micro data
> data("microData1", package="sdcTable")
> microData <- microData1; rm(microData1)
> # having a look at the data structure
> str(microData)
'data.frame':	100 obs. of  3 variables:
 $ region: chr  "C" "C" "A" "A" ...
 $ gender: chr  "male" "male" "male" "male" ...
 $ val   : num  9 11 10 11 18 10 6 9 5 12 ...
> 
> # we can observe that we have a micro data set consisting
> # of two spanning variables ('region' and 'gender') and one
> # numeric variable ('val')
> 
> # specify structure of hierarchical variable 'region'
> # levels 'A' to 'D' sum up to a Total
> dim.region <- data.frame(
+  levels=c('@','@@','@@','@@','@@'),
+  codes=c('Total', 'A','B','C','D'),
+  stringsAsFactors=FALSE)
> 
> # specify structure of hierarchical variable 'gender'
> # using create_node() and add_nodes() (see ?manage_hierarchies)
> dim.gender <- hier_create(root = "Total", nodes = c("male", "female"))
> hier_display(dim.gender)
Total
+-female
\-male
> 
> # create a named list with each element being a data-frame
> # containing information on one dimensional variable and
> # the names referring to variables in the input data
> dimList <- list(region=dim.region, gender=dim.gender)
> 
> # third column containts a numeric variable
> numVarInd <- 3
> 
> # no variables holding counts, numeric values, weights or sampling
> # weights are available in the input data
> freqVarInd <- weightInd <- sampWeightInd <- NULL
> 
> # creating an object of class \code{sdcProblem-class}
> problem <- makeProblem(
+  data=microData,
+  dimList=dimList,
+  freqVarInd=freqVarInd,
+  numVarInd=numVarInd,
+  weightInd=weightInd,
+  sampWeightInd=sampWeightInd)
Error in isFALSE(dt) : could not find function "isFALSE"
Calls: makeProblem -> hier_convert -> .to_df
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/seaaroundus.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/season.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 93.7Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.0Mb
Running 'testthat.R' [403s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 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(shar)
  > library(spatstat)
  Loading required package: spatstat.data
  Loading required package: nlme
  
  Attaching package: 'nlme'
  
  The following object is masked from 'package:dplyr':
  
      collapse
  
  Loading required package: rpart
  
  spatstat 1.58-2       (nickname: 'Not Even Wrong') 
  For an introduction to spatstat, type 'beginner' 
  
  
  Note: R version 3.4.4 (2018-03-15) is more than 9 months old; we strongly recommend upgrading to the latest version
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > 
  > test_check("shar")
  -- 1. Failure: Input raster can not be returned for randomize_raster (@test-rand
  any(list(landscape_classified) %in% landscape_random) isn't false.
  
  
  
  -- 2. Failure: Input raster can not be returned for translate_raster (@test-tran
  any(list(landscape_classified) %in% landscape_random) isn't false.
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 3 FAILED: 2
  1. Failure: Input raster can not be returned for randomize_raster (@test-randomize_raster.R#33) 
  2. Failure: Input raster can not be returned for translate_raster (@test-translate_raster.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    www   7.8Mb
Running examples in 'SID-Ex.R' failed
The error most likely occurred in:

> ### Name: randomDAG
> ### Title: outputs the adjacency matrix of a randomly generated directed
> ###   acyclic graph (DAG).
> ### Aliases: randomDAG
> ### Keywords: randomDAG causal (topological) order
> 
> ### ** Examples
> 
> randomDAG(p = 5, probConnect = 0.6)
5 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'SimInf-Ex.R' failed
The error most likely occurred in:

> ### Name: distance_matrix
> ### Title: Create a distance matrix between nodes for spatial models
> ### Aliases: distance_matrix
> 
> ### ** Examples
> 
> ## Generate a grid 10 x 10 and place one node in each cell
> ## separated by 100m.
> nodes <- expand.grid(x = (0:9) * 100, y = (0:9) * 100)
> plot(y ~ x, nodes)
> 
> ## Define the cutoff to only include neighbors within 300m.
> d <- distance_matrix(x = nodes$x, y = nodes$y, cutoff = 301)
> 
> ## View the first 10 rows and columns in the distance matrix
> d[1:10, 1:10]
10 x 10 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
ExpCatViz: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'SmartEDA-Ex.R' failed
The error most likely occurred in:

> ### Name: ExpCatViz
> ### Title: Distributions of categorical variables
> ### Aliases: ExpCatViz
> 
> ### ** Examples
> 
> ExpCatViz(data=mtcars,gp=NULL,fname=file.path(tempdir(),"Cat_1"),clim=10,margin=1,Page = c(2,2))
Error in isFALSE(rdata) : could not find function "isFALSE"
Calls: ExpCatViz
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-164 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
HardKMeansDemo: no visible global function definition for
  'graphics.off'
HardKMeansDemo: no visible global function definition for 'plot'
HardKMeansDemo: no visible global function definition for 'points'
initializeMeansMatrix: no visible global function definition for
  'runif'
initializeMeansMatrix: no visible global function definition for 'dist'
normalizeMatrix: no visible global function definition for 'sd'
plotRoughKMeans: no visible global function definition for
  'graphics.off'
plotRoughKMeans: no visible global function definition for 'plot'
plotRoughKMeans: no visible global function definition for 'points'
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Running examples in 'softImpute-Ex.R' failed
The error most likely occurred in:

> ### Name: SparseplusLowRank-class
> ### Title: Class '"SparseplusLowRank"'
> ### Aliases: SparseplusLowRank-class %*%,ANY,SparseplusLowRank-method
> ###   %*%,SparseplusLowRank,ANY-method %*%,Matrix,SparseplusLowRank-method
> ###   %*%,SparseplusLowRank,Matrix-method
> ###   as.matrix,SparseplusLowRank-method colMeans,SparseplusLowRank-method
> ###   colSums,SparseplusLowRank-method dim,SparseplusLowRank-method
> ###   norm,SparseplusLowRank,character-method
> ###   rowMeans,SparseplusLowRank-method rowSums,SparseplusLowRank-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("SparseplusLowRank")
Class "SparseplusLowRank" [package "softImpute"]

Slots:
                                             
Name:             x            a            b
Class: sparseMatrix       matrix       matrix
> x=matrix(sample(c(3,0),15,replace=TRUE),5,3)
> x=as(x,"sparseMatrix")
> a=matrix(rnorm(10),5,2)
> b=matrix(rnorm(6),3,2)
> new("SparseplusLowRank",x=x,a=a,b=b)
An object of class "SparseplusLowRank"
Slot "x":
5 x 3 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 118-120 (softImpute.Rmd) 
Error: processing vignette 'softImpute.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running 'test-all.R' [199s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
    Using cached copy of .inputObjects event in test module.   
  -- 1. Failure: simulation runs with simInit and spades (@test-simulation.R#86)  
  mySim$caribou$x not equivalent to `pos_x`.
  100/100 mismatches (average diff: 9.83)
  [1]   3.67 -   1.06 ==   2.613
  [2]  43.57 -  44.45 ==  -0.883
  [3]  47.23 -  45.88 ==   1.351
  [4]   3.60 -  -1.32 ==   4.918
  [5]  20.23 -  17.86 ==   2.370
  [6] -47.81 -  48.48 == -96.294
  [7]  16.55 -  10.75 ==   5.796
  [8] -21.41 - -24.63 ==   3.218
  [9] -47.28 - -48.51 ==   1.234
  ...
  
  -- 2. Failure: simulation runs with simInit and spades (@test-simulation.R#87)  
  mySim$caribou$y not equivalent to `pos_y`.
  100/100 mismatches (average diff: 5.15)
  [1] -15.00 - -15.90 ==  0.898
  [2]  -5.35 -  -8.97 ==  3.616
  [3]  19.51 -  25.27 == -5.758
  [4] -36.40 - -39.07 ==  2.674
  [5] -33.64 - -32.96 == -0.678
  [6]  15.57 -  19.59 == -4.027
  [7]  15.12 -  14.87 ==  0.249
  [8]  39.63 -  38.26 ==  1.368
  [9]  -6.33 -  -8.17 ==  1.831
  ...
  
    Using cached copy of .inputObjects event in child6 module.   
    Using memoised copy of .inputObjects event in child6 module
    Using memoised copy of .inputObjects event in child6 module
  == testthat results  ===========================================================
  OK: 458 SKIPPED: 32 FAILED: 2
  1. Failure: simulation runs with simInit and spades (@test-simulation.R#86) 
  2. Failure: simulation runs with simInit and spades (@test-simulation.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
sgmix: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'spagmix-Ex.R' failed
The error most likely occurred in:

> ### Name: lgcpmix
> ### Title: Generate a spatial log-Gaussian Cox process intensity
> ### Aliases: lgcpmix
> 
> ### ** Examples
> 
> ## Homogeneous example ##
> 
> # Create constant intensity image integrating to 500
> 
> homog <- as.im(as.mask(toywin))
> homog <- homog/integral(homog)*500
> 
> 
> # Corresponding LGCP realisations using exponential covariance structure
> par(mfrow=c(2,2),mar=rep(1.5,4))
> for(i in 1:4){
+   temp <- lgcpmix(homog,covmod="exp",covpars=list(var=1,scale=0.2))
+   plot(temp,main=paste("Realisation",i),log=TRUE)
+ }
> 
> 
> 
> ## Inhomogeneous examples ##
> 
> # Create deterministic trend
> 
> mn <- cbind(c(0.25,0.8),c(0.31,0.82),c(0.43,0.64),c(0.63,0.62),c(0.21,0.26))
> v1 <- matrix(c(0.0023,-0.0009,-0.0009,0.002),2)
> v2 <- matrix(c(0.0016,0.0015,0.0015,0.004),2)
> v3 <- matrix(c(0.0007,0.0004,0.0004,0.0011),2)
> v4 <- matrix(c(0.0023,-0.0041,-0.0041,0.0099),2)
> v5 <- matrix(c(0.0013,0.0011,0.0011,0.0014),2)
> vr <- array(NA,dim=c(2,2,5))
> for(i in 1:5) vr[,,i] <- get(paste("v",i,sep=""))
> intens <- sgmix(mean=mn,vcv=vr,window=toywin,p0=0.1,int=500)
Error in isFALSE(all.equal(sum(c(0.3, p)), 1)) : 
  could not find function "isFALSE"
Calls: sgmix
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sparsebnUtils
Loading required package: ccdrAlgorithm
Loading required package: discretecdAlgorithm

sparsebn v0.0.5, Copyright (c) 2016-2017
	Bryon Aragam, University of California, Los Angeles
	Jiaying Gu, University of California, Los Angeles
	Dacheng Zhang, University of California, Los Angeles
	Qing Zhou, University of California, Los Angeles
	Fei Fu

Please cite our work! Type citation("sparsebn") for details.
---> Bugs? Please report any bugs at https://github.com/itsrainingdata/sparsebn/issues.

A list of interventions was not specified: Assuming data is purely observational.
Quitting from lines 184-186 (sparsebn-vignette.Rmd) 
Error: processing vignette 'sparsebn-vignette.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Running examples in 'sparseinv-Ex.R' failed
The error most likely occurred in:

> ### Name: cholPermute
> ### Title: Sparse Cholesky factorisation with fill-in reducing permutations
> ### Aliases: cholPermute
> ### Keywords: Cholesky factor
> 
> ### ** Examples
> 
> require(Matrix)
Loading required package: Matrix
> cholPermute(sparseMatrix(i = c(1,1,2,2),
+                          j = c(1, 2, 1, 2),
+                          x = c(0.1, 0.2, 0.2, 1)))
$Qpermchol
2 x 2 sparse Matrix of class "dtCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print -> print -> .local
Execution halted
Running examples in 'sparsestep-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.sparsestep
> ### Title: Get the coefficients of a fitted SparseStep model
> ### Aliases: coef coef.sparsestep
> 
> ### ** Examples
> 
> x <- matrix(rnorm(100*20), 100, 20)
> y <- rnorm(100)
> fit <- sparsestep(x, y)
> coef(fit)
21 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'sparsesvd-Ex.R' failed
The error most likely occurred in:

> ### Name: sparsesvd
> ### Title: Singular Value Decomposition of a Sparse Matrix.
> ### Aliases: sparsesvd
> 
> ### ** Examples
> 
> M <- rbind(
+   c(20, 10, 15,  0,  2),
+   c(10,  5,  8,  1,  0),
+   c( 0,  1,  2,  6,  3),
+   c( 1,  0,  0, 10,  5))
> M <- Matrix::Matrix(M, sparse=TRUE)
> print(M)
4 x 5 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: print ... print.default -> <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.0Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/spcosa.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/spmoran.Rcheck/00install.out' for details.
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'spotifyr-Ex.R'
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
Running examples in 'SSBtools-Ex.R' failed
The error most likely occurred in:

> ### Name: DummyHierarchy
> ### Title: Converting hierarchy specifications to a (signed) dummy matrix
> ### Aliases: DummyHierarchy
> 
> ### ** Examples
> 
> # A hierarchy table
> h <- SSBtoolsData("FIFA2018ABCD")
> 
> DummyHierarchy(h$mapsFrom, h$mapsTo, h$sign, h$level)
9 x 16 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'stability-Ex.R'
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Running examples in 'sybil-Ex.R' failed
The error most likely occurred in:

> ### Name: addReact,modelorg-method
> ### Title: Add/Change Reactions in a Model
> ### Aliases: addReact addReact,modelorg-method addReact,modelorg,ANY-method
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(Ec_core)
> 
> # add reaction A + 2 B <-> C to the model
> modelNew <- addReact(Ec_core, id="newReact", met=c("A", "B", "C"),
+ 						Scoef=c(-1, -2, 1), reversible=TRUE,
+ 						lb=-1000, ub=1000, obj=0)
> 
> # view the new reaction
> shrinkMatrix(modelNew, j="newReact")
3 x 1 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running examples in 'syt-Ex.R' failed
The error most likely occurred in:

> ### Name: syt2matrix
> ### Title: Standard Young tableau as sparse matrix
> ### Aliases: syt2matrix
> 
> ### ** Examples
> 
> syt <- list(c(1,2,6), c(3,5), 4)
> syt2matrix(syt)
3 x 3 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  -- 1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  cannot open URL 'http://www.europarl.europa.eu/oeil/popups/printfichetechnical.pdf?id=673511&lang=fr'
  1: extract_text(f2, page = 1, encoding = "latin1") at testthat/test_non-latin.R:15
  2: load_doc(file, password = password, copy = copy)
  3: localize_file(path = file, copy = copy)
  4: utils::download.file(path, tmp, quiet = quiet, mode = "wb")
  
  == testthat results  ===========================================================
  OK: 90 SKIPPED: 0 FAILED: 1
  1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...

Attaching package: 'tensorr'

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

    norm

Quitting from lines 170-172 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running examples in 'textir-Ex.R' failed
The error most likely occurred in:

> ### Name: srproj
> ### Title: Multinomial Inverse Regression (MNIR)
> ### Aliases: mnlm srproj
> 
> ### ** Examples
> 
> 
> ### Ripley's Cushing Data; see help(Cushings) ###
> library(MASS)
> data(Cushings)
> Cushings[,1:2] <- log(Cushings[,1:2])
> train <- Cushings[Cushings$Type!="u",]
> newdata <- as.matrix(Cushings[Cushings$Type == "u", 1:2])
> 
> ## fit, coefficients, predict, and plot
> 
> # you could replace 'mnlm' with 'dmr' here.
> fit <- mnlm(NULL, 
+   covars=train[,1:2], 
+   counts=factor(train$Type))
> 
> ## dmr applies corrected AICc selection by default
> round(coef(fit),1) 
3 x 3 sparse Matrix of class "dmrcoef"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 1224-1238 (functionality_of_textTinyR_package.Rmd) 
Error: processing vignette 'functionality_of_textTinyR_package.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Package unavailable to check Rd xrefs: 'Rpoppler'
Missing link or links in documentation object 'hpc.Rd':
  '[parallel:getDefaultCluster]{getDefaultCluster}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    doc       2.7Mb
    extdata   8.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/treemap.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: trustOptim
Quitting from lines 125-129 (trustOptim-demo.Rmd) 
Error: processing vignette 'trustOptim-demo.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.2Mb
Running examples in 'udpipe-Ex.R' failed
The error most likely occurred in:

> ### Name: as.matrix.cooccurrence
> ### Title: Convert the result of cooccurrence to a sparse matrix
> ### Aliases: as.matrix.cooccurrence
> 
> ### ** Examples
> 
> data(brussels_reviews_anno)
> ## By document, which lemma's co-occur
> x <- subset(brussels_reviews_anno, xpos %in% c("NN", "JJ") & language %in% "fr")
> x <- cooccurrence(x, group = "doc_id", term = "lemma")
> x <- as.matrix(x)
> dim(x)
[1] 1199 1199
> x[1:3, 1:3]
3 x 3 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Packages required and available but unsuitable versions: 'grDevices' 'grid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/UpSetR.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
Running examples in 'vcrpart-Ex.R' failed
The error most likely occurred in:

> ### Name: contr.wsum
> ### Title: Contrast matrices
> ### Aliases: contr.wsum
> 
> ### ** Examples
> 
> x <- factor(rep(LETTERS[1:3], c(10, 20, 30)))
> contr.wsum(x) # standard call
           A          B
A  1.0000000  0.0000000
B  0.0000000  1.0000000
C -0.3333333 -0.6666667
> contr.wsum(x, sparse = TRUE) # using a sparse matrix
3 x 2 sparse Matrix of class "dgCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Error in re-building vignettes:
  ...
trying URL 'https://germansl.infinitenature.org/GermanSL/1.3/GermanSL.zip'
Content type 'application/zip' length 3042090 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

Warning in isc(elbaue, trait.db = eco, ivname = "OEK_F", method = "mean") :
  Detecting 0 values, please check.
Warning in isc(elbaue, trait.db = eco, ivname = "OEK_N", method = "mean") :
  Detecting 0 values, please check.
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "vegdata.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'vegdata.tex' failed

LaTeX errors:
a.tex:437: Package inputenc Error: Unicode char Â (U+81)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help
a.tex:437: Package inputenc Error: Unicode char Â (U+81)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help
a.tex:437: Package inputenc Error: Unicode char Â (U+81)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.2Mb
    help   2.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Running examples in 'wordspace-Ex.R' failed
The error most likely occurred in:

> ### Name: DSM_TermContextMatrix
> ### Title: Example of a Term-Context Co-occurrence Matrix (wordspace)
> ### Aliases: DSM_TermContextMatrix DSM_TermContext
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> DSM_TermContextMatrix["time", ] # row vector for target noun "time"
   Felidae        Pet      Feral       Boat Philosophy       Kant  Back_Pain 
         1          0          0          2          2          1          0 
> 
> all.equal(DSM_TermContextMatrix, head(DSM_TermContext, Inf))
[1] TRUE
> 
> # M M' = symmetric matrix of co-occurrence frequencies of nouns within articles
> tcrossprod(DSM_TermContextMatrix) 
7 x 7 sparse Matrix of class "dsCMatrix"
Error in isFALSE(suppRows) : could not find function "isFALSE"
Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
Execution halted
Running 'dist_matrix.R' [3s]
  Running 'dsm_projection.R' [4s]
  Running 'dsm_score.R' [4s]
  Running 'file_formats.R' [3s]
Running the tests in 'tests/file_formats.R' failed.
Complete output:
  > ## Test reading data sets in different file formats, based on the example DSM_TermContext matrix
  > 
  > library(wordspace)
  Loading required package: Matrix
  > 
  > ## example data: DSM_TermContext
  > TC <- DSM_TermContext        # order rows and columns alphabetically for comparison with input files
  > idxR <- order(TC$rows$term)
  > idxC <- order(TC$cols$term)
  > TC$M <- TC$M[idxR, idxC]
  > TC$rows <- TC$rows[idxR, ]
  > TC$cols <- TC$cols[idxC, ]
  > invisible(check.dsm(TC, validate=TRUE))
  > head(TC, Inf)
  7 x 7 sparse Matrix of class "dgCMatrix"
  Error in isFALSE(suppRows) : could not find function "isFALSE"
  Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
  Execution halted
Running 'dist_matrix.R' [4s]
  Running 'dsm_projection.R' [5s]
  Running 'dsm_score.R' [4s]
  Running 'file_formats.R' [3s]
Running the tests in 'tests/file_formats.R' failed.
Complete output:
  > ## Test reading data sets in different file formats, based on the example DSM_TermContext matrix
  > 
  > library(wordspace)
  Loading required package: Matrix
  > 
  > ## example data: DSM_TermContext
  > TC <- DSM_TermContext        # order rows and columns alphabetically for comparison with input files
  > idxR <- order(TC$rows$term)
  > idxC <- order(TC$cols$term)
  > TC$M <- TC$M[idxR, idxC]
  > TC$rows <- TC$rows[idxR, ]
  > TC$cols <- TC$cols[idxC, ]
  > invisible(check.dsm(TC, validate=TRUE))
  > head(TC, Inf)
  7 x 7 sparse Matrix of class "dgCMatrix"
  Error in isFALSE(suppRows) : could not find function "isFALSE"
  Calls: <Anonymous> -> <Anonymous> -> printSpMatrix2
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: Matrix
Quitting from lines 84-85 (wordspace-intro.Rmd) 
Error: processing vignette 'wordspace-intro.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Error in re-building vignettes:
  ...
Loading required package: xgboost
Loading required package: Matrix
Loading required package: data.table
Loading required package: vcd
Loading required package: grid
Quitting from lines 150-152 (discoverYourData.Rmd) 
Error: processing vignette 'discoverYourData.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/zonator.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/3.4/abcdeFBA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘HH’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    6.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/acebayes.Rcheck/00install.out’ for details.
Packages required but not available: ‘aroma.affymetrix’ ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
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 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
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/3.4/adamethods.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/adaptivetau.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/adiv.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/adpss.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/3.4/AFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/AgreementInterval.Rcheck/00install.out’ for details.
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/3.4/AIG.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algebraichaplo.tex' failed.
LaTeX errors:
! LaTeX Error: File `ngerman.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [square,comma, numbers,sort&compress]{natbib}   % numbers wor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'alleHap.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \setcounter
                {secnumdepth}{5}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.14-377 created on 2019-03-04.
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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ammistability.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/psnfss/times.sty)

! LaTeX Error: File `xy.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make: *** [anchors.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/anchors.Rcheck/vign_test/anchors") : 
  running 'make' failed
Execution halted
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ANOM.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Missing or unexported object: ‘rhdf5::h5closeAll’
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/3.4/Anthropometry.Rcheck/00install.out’ for details.
Package required but not available: ‘BiocManager’

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

> ### Name: apa.reg.table
> ### Title: Creates a regresion table in APA style
> ### Aliases: apa.reg.table
> 
> ### ** Examples
> 
> # View top few rows of goggles data set
> # from Discovering Statistics Using R
> head(album)
   adverts sales airplay attract
1   10.256   330      43      10
2  985.685   120      28       7
3 1445.563   360      35       7
4 1188.193   270      33       7
5  574.513   220      44       5
6  568.954   170      19       5
> 
> # Single block example
> blk1 <- lm(sales ~ adverts + airplay, data=album)
> apa.reg.table(blk1)
Error in if (number_predictors > 1) { : argument is of length zero
Calls: apa.reg.table -> apa_single_block
Execution halted
installed size is 93.3Mb
  sub-directories of 1Mb or more:
    libs  92.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apsimr-basics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: gWidgets
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apt.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [pdftex]{graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=15: zs > maxKappa
Warning in axis(1, at = a, ...) : "axes" is not a graphical parameter
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'archetypes.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: ‘aroma.core’ ‘PSCBS’

Packages suggested but not available for checking: ‘aroma.light’ ‘GLAD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/3.4/Arothron.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [26s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 336 SKIPPED: 0 FAILED: 27
  1. Error: ordinal works (@test_modelsum.R#158) 
  2. Failure: write2.tableby -> HTML (@test_write2.R#28) 
  3. Failure: write2.tableby -> HTML (@test_write2.R#28) 
  4. Failure: write2.modelsum -> HTML (@test_write2.R#34) 
  5. Failure: write2.modelsum -> HTML (@test_write2.R#34) 
  6. Failure: write2.freqlist -> HTML (@test_write2.R#42) 
  7. Failure: write2.freqlist -> HTML (@test_write2.R#42) 
  8. Failure: write2.freqlist -> doc (@test_write2.R#47) 
  9. Failure: write2.freqlist -> doc (@test_write2.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Error in re-building vignettes:
  ...
Loading required package: ASPBay
Loading required package: hexbin
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ASPBay.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘org.Hs.eg.db’ ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘BiocManager’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BACA.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Loading required package: BACCO
Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Loading required package: approximator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'both_papers.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bamp.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

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/3.4/BAT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bayesCL.Rcheck/00install.out’ for details.
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
 **********   MAMS Version 1.01********** 

Type MAMSNews() to see new features/changes/bug fixes.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BayesFreq.tex' failed.
LaTeX errors:
! LaTeX Error: File `doi.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  14.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: splines
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbefkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbemkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bcaboot.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: plyr
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcpa.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.9Mb
Package suggested but not available for checking: ‘beadarrayExampleData’
installed size is 57.8Mb
  sub-directories of 1Mb or more:
    libs  56.4Mb
Package required and available but unsuitable version: ‘ufs’

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/3.4/benchmarkme.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
For more information on the usage of the BEQI2 tool, type: vignette("BEQI2")
Number of duplicated records: 1
These will be removed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BEQI2.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.74 \allsectionsfont
                     {\sffamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
adjustPL: no visible global function definition for ‘ergm_model’
adjustPL: no visible global function definition for ‘ergm_proposal’
adjustPL: no visible global function definition for ‘ergm_MCMC_slave’
adjustPL : <anonymous>: no visible global function definition for
  ‘ergm_MCMC_slave’
bergm: no visible global function definition for ‘ergm_model’
bergm: no visible global function definition for ‘ergm_proposal’
bergm: no visible global function definition for ‘ergm_MCMC_slave’
calibrate.bergm: no visible global function definition for ‘ergm_model’
calibrate.bergm: no visible global function definition for
  ‘ergm_proposal’
calibrate.bergm : robinsmon.ergm: no visible global function definition
  for ‘ergm_model’
calibrate.bergm : robinsmon.ergm: no visible global function definition
  for ‘ergm_proposal’
calibrate.bergm : robinsmon.ergm: no visible global function definition
  for ‘ergm_MCMC_slave’
calibrate.bergm: no visible global function definition for
  ‘ergm_MCMC_slave’
evidence_CJ : mspecs: no visible global function definition for
  ‘ergm_model’
evidence_PP : mspecs: no visible global function definition for
  ‘ergm_model’
missBergm: no visible global function definition for ‘ergm_model’
missBergm: no visible global function definition for ‘ergm_proposal’
missBergm: no visible global function definition for ‘ergm_MCMC_slave’
Undefined global functions or variables:
  ergm_MCMC_slave ergm_model ergm_proposal
Running examples in ‘Bergm-Ex.R’ failed
The error most likely occurred in:

> ### Name: bergm
> ### Title: Parameter estimation for Bayesian ERGMs
> ### Aliases: bergm
> 
> ### ** Examples
> 
> # Load the florentine marriage network
> data(florentine)
> 
> # Posterior parameter estimation:
> 
> p.flo <- bergm(flomarriage ~ edges + kstar(2),
+                burn.in = 50,
+                aux.iters = 500,
+                main.iters = 500,
+                gamma = 1)
Error in ergm_model(formula, y) : could not find function "ergm_model"
Calls: bergm
Execution halted
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bfsl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bfw.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BGLR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BHMSMAfMRIvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {latexsym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [3s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10006 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.7Mb
Package suggested but not available for checking: ‘RODBC’
Error in re-building vignettes:
  ...
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 is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in normalizePath(f2) :
  path[1]="./webshot16c302e234bc7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c302e234bc7.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘parallel’

Package suggested but not available for checking: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bigstep.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.5Mb
Error in re-building vignettes:
  ...
Loading required package: diptest
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bioacoustics.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BiocManager.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/3.4/Biocomb.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [7s/7s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘ChemmineR’ ‘fmcsR’ ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/3.4/BiSEp.Rcheck/00install.out’ for details.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BMAmevt.tex' failed.
LaTeX errors:
! LaTeX Error: File `cases.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  43.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bms.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \setpapersize
                 {A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BMTME.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...

    dexp, dgamma, dweibull, pexp, pgamma, pweibull, qexp, qgamma,
    qweibull, rexp, rgamma, rweibull

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

    precip

Loading required package: BoolNet
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BoolFilter.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 322.8Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      319.5Mb
installed size is 68.2Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bpbounds.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/3.4/bpca.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 the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Running ‘testthat.R’ [6s/6s]
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
Running ‘test-all.R’ [45s/45s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 195 SKIPPED: 0 FAILED: 16
  1. Failure: (unknown) (@test-alltibbles.R#54) 
  2. Failure: (unknown) (@test-alltibbles.R#54) 
  3. Failure: (unknown) (@test-alltibbles.R#54) 
  4. Failure: (unknown) (@test-alltibbles.R#54) 
  5. Failure: (unknown) (@test-alltibbles.R#53) 
  6. Failure: (unknown) (@test-alltibbles.R#53) 
  7. Failure: (unknown) (@test-alltibbles.R#53) 
  8. Failure: (unknown) (@test-alltibbles.R#54) 
  9. Failure: (unknown) (@test-alltibbles.R#54) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> ### Name: tidy.garch
> ### Title: Tidy a(n) garch object
> ### Aliases: tidy.garch garch_tidiers
> 
> ### ** Examples
> 
> 
> library(tseries)
Error: package or namespace load failed for ‘tseries’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/xts/libs/xts.so':
  `maximal number of DLLs reached...
Execution halted
Missing link or links in documentation object 'phylomatic_names.Rd':
  ‘[taxize:use_entrez]{taxize::use_entrez()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Brundle.Rcheck/00install.out’ for details.
installed size is 22.6Mb
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installed size is 77.2Mb
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Package suggested but not available for checking: ‘gsl’
installed size is 18.7Mb
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Error in re-building vignettes:
  ...

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]="./webshot5d7250e1c985.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5d7250e1c985.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
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cairoDevice.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Cairo.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CalibrationGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ncdf4’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.3-6, (SVN revision 773)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.3-1 
Warning in engine$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 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
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Execution halted
Packages suggested but not available for checking:
  ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Error in re-building vignettes:
  ...
Removing 14 individuals due to missing phenotypes.


2 marker(s) rejected due to linear non-independence.
 For more information see markers.removed.for.non.independence.txt
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cape.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
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    libs   3.0Mb
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Error in re-building vignettes:
  ...
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

     Hanna Meyer, Christoph Reudenbach, Marvin Ludwig, Thomas Nauss
     _Maintainer:_ Hanna Meyer <email: hanna.meyer@geo.uni-marburg.de>


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]="./webshot132115399a70d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot132115399a70d.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted