Running ‘genotype_test.R’ [1s/1s]
  Comparing ‘genotype_test.Rout’ to ‘genotype_test.Rout.save’ ... OK
  Running ‘test_code_example.R’ [1s/2s]
Running the tests in ‘tests/test_code_example.R’ failed.
Complete output:
  > ## Test code example 1 from 
  > ## Gjuvsland AB, Wang Y, Plahte E, Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Submitted to Frontiers in Genetics
  > 
  > library(gpmap)
  Loading required package: isotone
  Loading required package: plyr
  Loading required package: ggplot2
  Loading required package: foreach
  > data(GPmaps)
  > gp <- mouseweight
  > 
  > ## Tabulate genotypic values
  > cbind(gp$genotype,gp$values)
    Locus_B Locus_A LG_JxSM_J
  1    B1B1    A1A1    36.839
  2    B1B2    A1A1    36.527
  3    B2B2    A1A1    33.824
  4    B1B1    A1A2    37.951
  5    B1B2    A1A2    35.898
  6    B2B2    A1A2    34.125
  7    B1B1    A2A2    34.118
  8    B1B2    A2A2    34.894
  9    B2B2    A2A2    31.234
  > 
  > ## Plot the GP map
  > plot(gp)		
  [[1]]
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
  Execution halted
Running examples in ‘gppm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.LongData
> ### Title: Plot a Long Data Frame
> ### Aliases: plot.LongData
> 
> ### ** Examples
> 
> data("demoLGCM")
> plot(demoLGCM,plotIds=c(1,2,3))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘gprofiler2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gostplot
> ### Title: Manhattan plot of functional enrichment results.
> ### Aliases: gostplot
> 
> ### ** Examples
> 
>  gostres <- gost(c("Klf4", "Pax5", "Sox2", "Nanog"), organism = "mmusculus")
>  gostplot(gostres)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: gostplot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Quitting from lines 39-51 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: granovagg.1w
> ### Title: Elemental Graphic Display for One-Way ANOVA
> ### Aliases: granovagg.1w
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> data(arousal)
> #Drug A
> granovagg.1w(arousal[,1:2], h.rng = 1.6, v.rng = 0.5)

By-group summary statistics for your input data (ordered by group means)
    group group.mean trimmed.mean contrast variance standard.deviation
1 Placebo      20.43        20.30    -1.92     5.83               2.41
2  Drug.A      24.27        24.45     1.92     7.89               2.81
  group.size
1         10
2         10

Below is a t-test summary of your input data

	Two Sample t-test

data:  unstacked.data[, 1] and unstacked.data[, 2]
t = -3.2786, df = 18, p-value = 0.004174
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
 -6.300681 -1.379319
sample estimates:
mean of x mean of y 
    20.43     24.27 

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom_generators.Rmd’ using rmarkdown
Quitting from lines 50-56 (custom_generators.Rmd) 
Error: processing vignette 'custom_generators.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘custom_generators.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 42-51 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘piping.Rmd’ using rmarkdown
Quitting from lines 26-37 (piping.Rmd) 
Error: processing vignette 'piping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘piping.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: appraise
> ### Title: Model diagnostic plots
> ### Aliases: appraise
> 
> ### ** Examples
> 
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
> ## Don't show: 
> set.seed(2)
> ## End(Don't show)
> ## simulate some data...
> dat <- gamSim(1, n = 400, dist = "normal", scale = 2)
Gu & Wahba 4 term additive model
> mod <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
> ## run some basic model checks, including checking
> ## smoothing basis dimensions...
> appraise(mod)
Error in pSummary(..., op = "max") : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: appraise ... plot_grid -> align_plots -> do.call -> <Anonymous> -> pSummary
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘printCrudeAndAdjustedModel.Rmd’ using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: magrittr
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

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

--- re-building ‘timeSplitter.Rmd’ using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable

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 coxpenal.fit(X, Y, strats, offset, init = init, control, weights = weights,  :
  Inner loop failed to coverge for iterations 3
Quitting from lines 500-523 (timeSplitter.Rmd) 
Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘timeSplitter.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gremlin-package
> ### Title: Mixed-Effects REML Incorporating Generalized Inverses
> ### Aliases: gremlin-package _PACKAGE
> 
> ### ** Examples
> 
>   require(nadiv)
Loading required package: nadiv
>   Ainv <- makeAinv(Mrode3[-c(1:2), 1:3])$Ainv
>   mod11 <- gremlinR(WWG11 ~ sex - 1,
+ random = ~ calf,
+ data = Mrode11,
+ ginverse = list(calf = Ainv),
+ Gstart = matrix(0.2), Rstart = matrix(0.4),
+ maxit = 10, v = 2)
gremlin started:		 21:31:47 
   1 of max 10 			 21:31:47 
	EM to find next theta
Element 0.2124631 must be a symmetric matrix or a number
Error in FUN(X[[i]], ...) : 
Calls: gremlinR -> sapply -> lapply -> FUN
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘arrangeGrob.rmd’ using rmarkdown
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette 'arrangeGrob.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘arrangeGrob.rmd’

--- re-building ‘gtable.Rmd’ using rmarkdown
Loading required package: knitr
Loading required package: gridExtra
Loading required package: grid
Loading required package: gtable
Loading required package: ggplot2
Quitting from lines 52-55 (gtable.Rmd) 
Error: processing vignette 'gtable.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtable.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘arrangeGrob.rmd’ ‘gtable.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_multiple_n_persons_x_times
> ### Title: Draw and redraw results of simulation
> ### Aliases: draw_multiple_n_persons_x_times
> 
> ### ** Examples
> 
> ## simulate
> prob <-  dexp(1:30, .05)      # probabilities for categories
> N <- seq(10, 80, by = 10)     # smaple sizes to simulate
> r <- sim_n_persons_x_times_many_n(prob, n = N, a = 7, times = 100, progress = "none")
> 
> # calculate and draw
> M <- 1:5                      # minimal number of categories to evaluate
> p <- c(0.9, .95, 1)           # proportion of categories for which minimal m holds
> d <- calc_probabilities(r, n = N, ms = M, min.props = p)
> draw_multiple_n_persons_x_times(d)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Growthcurver-vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 397-414 (Growthcurver-vignette.Rmd) 
Error: processing vignette 'Growthcurver-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Growthcurver-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gsSurvTemplate.rnw’ using knitr
Loading required package: gsDesign
Loading required package: xtable
Loading required package: ggplot2
Quitting from lines 146-147 (gsSurvTemplate.rnw) 
Error: processing vignette 'gsSurvTemplate.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gsSurvTemplate.rnw’

--- re-building ‘gsSurvTemplateInstructions.rnw’ using knitr
Loading required package: gsDesign
Loading required package: xtable
Loading required package: ggplot2
Quitting from lines 183-184 (gsSurvTemplateInstructions.rnw) 
Error: processing vignette 'gsSurvTemplateInstructions.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gsSurvTemplateInstructions.rnw’

SUMMARY: processing the following files failed:
  ‘gsSurvTemplate.rnw’ ‘gsSurvTemplateInstructions.rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lisiecki2005
> ### Title: LR04 Global Pliocene-Pleistocene Benthic d18O Stack (5.3-Myr).
> ### Aliases: lisiecki2005
> ### Keywords: datasets
> 
> ### ** Examples
> 
> names(lisiecki2005)
[1] "Time"  "d18O"  "Error"
> head(lisiecki2005)
  Time d18O Error
1    0 3.23  0.03
2    1 3.23  0.04
3    2 3.18  0.03
4    3 3.29  0.03
5    4 3.30  0.03
6    5 3.26  0.03
> # plot for 0-250 ka:
> if (require("ggplot2")) {
+    ggplot(lisiecki2005,
+           aes(Time,
+               d18O)) +
+      geom_line() +
+      scale_x_continuous(limits = c(0, 250),
+                         name = "x 1000 years ago") +
+      scale_y_reverse(name = bquote(delta^18*O)) +
+      theme_bw()
+    }
Loading required package: ggplot2
Warning: Removed 1864 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: Removed 1864 rows containing missing values (geom_path).
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GSODR.Rmd’ using rmarkdown
Quitting from lines 129-147 (GSODR.Rmd) 
Error: processing vignette 'GSODR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GSODR.Rmd’

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

--- re-building ‘use_case_1.Rmd’ using rmarkdown
--- finished re-building ‘use_case_1.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gunsales.Rmd’ using rmarkdown
Quitting from lines 60-61 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gunsales.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hapiCVDistance
> ### Title: Histogram of crossover distance
> ### Aliases: hapiCVDistance
> 
> ### ** Examples
> 
> data(crossover)
> hapiCVDistance(cv=crossover)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘A_Haplin_intro_installation.Rmd’ using rmarkdown
--- finished re-building ‘A_Haplin_intro_installation.Rmd’

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

--- re-building ‘C_Running_Haplin.Rmd’ using rmarkdown
Read 6 items
Read 1494 items
Read 0 items
Read 8 items
Read 9112 items
Read 0 items
Read 864 items
Read 1433376 items
Read 0 items
Quitting from lines 141-142 (C_Running_Haplin.Rmd) 
Error: processing vignette 'C_Running_Haplin.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘C_Running_Haplin.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hp
> ### Title: Harry Potter Colour Map.
> ### Aliases: hp hp_pal harrypotter
> 
> ### ** Examples
> 
> library(ggplot2)
> library(hexbin)
> 
> dat <- data.frame(x = rnorm(1e4), y = rnorm(1e4))
> ggplot(dat, aes(x = x, y = y)) +
+   geom_hex() +
+   coord_fixed() +
+   scale_fill_gradientn(colours = hp(128, option = 'Always'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [24s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 2. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 4. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 5. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
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-patched-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘hazus_demo.Rmd’ using knitr
Quitting from lines 109-119 (hazus_demo.Rmd) 
Error: processing vignette 'hazus_demo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hazus_demo.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv_corrected_lasso
> ### Title: Cross-validated Corrected lasso
> ### Aliases: cv_corrected_lasso
> 
> ### ** Examples
> 
> # Gaussian
> set.seed(100)
> n <- 100; p <- 50 # Problem dimensions
> # True (latent) variables
> X <- matrix(rnorm(n * p), nrow = n)
> # Measurement error covariance matrix
> # (typically estimated by replicate measurements)
> sigmaUU <- diag(x = 0.2, nrow = p, ncol = p)
> # Measurement matrix (this is the one we observe)
> W <- X + rnorm(n, sd = diag(sigmaUU))
> # Coefficient
> beta <- c(seq(from = 0.1, to = 1, length.out = 5), rep(0, p-5))
> # Response
> y <- X %*% beta + rnorm(n, sd = 1)
> # Run the corrected lasso
> cvfit <- cv_corrected_lasso(W, y, sigmaUU, no_radii = 5, n_folds = 3)
> plot(cvfit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdme-package.Rmd’ using rmarkdown

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union


Attaching package: 'zeallot'

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

    %->%, %<-%

Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Attaching package: 'dplyr'

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

    as_data_frame, groups, union

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 156-162 (hdme-package.Rmd) 
Error: processing vignette 'hdme-package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hdme-package.Rmd’

SUMMARY: processing the following file failed:
  ‘hdme-package.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rlassoEffects
> ### Title: rigorous Lasso for Linear Models: Inference
> ### Aliases: rlassoEffects rlassoEffects.default rlassoEffects.formula
> ###   rlassoEffect
> 
> ### ** Examples
> 
> library(hdm); library(ggplot2)
> set.seed(1)
> n = 100 #sample size
> p = 100 # number of variables
> s = 3 # nubmer of non-zero variables
> X = matrix(rnorm(n*p), ncol=p)
> colnames(X) <- paste("X", 1:p, sep="")
> beta = c(rep(3,s), rep(0,p-s))
> y = 1 + X%*%beta + rnorm(n)
> data = data.frame(cbind(y,X))
> colnames(data)[1] <- "y"
> fm = paste("y ~", paste(colnames(X), collapse="+"))
> fm = as.formula(fm)                 
> lasso.effect = rlassoEffects(X, y, index=c(1,2,3,50))
> lasso.effect = rlassoEffects(fm, I = ~ X1 + X2 + X3 + X50, data=data)
> print(lasso.effect)

Call:
rlassoEffects.formula(formula = fm, data = data, I = ~X1 + X2 + 
    X3 + X50)

Coefficients:
     X1       X2       X3      X50  
2.94448  3.04127  2.97540  0.07196  

> summary(lasso.effect)
[1] "Estimates and significance testing of the effect of target variables"
    Estimate. Std. Error t value Pr(>|t|)    
X1    2.94448    0.08815  33.404   <2e-16 ***
X2    3.04127    0.08389  36.253   <2e-16 ***
X3    2.97540    0.07804  38.127   <2e-16 ***
X50   0.07196    0.07765   0.927    0.354    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1


> confint(lasso.effect)
          2.5 %    97.5 %
X1   2.77171308 3.1172421
X2   2.87685121 3.2056979
X3   2.82244962 3.1283583
X50 -0.08022708 0.2241377
> plot(lasso.effect)
Warning: Ignoring unknown aesthetics: width, h
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘hdnom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hdnom.calibrate
> ### Title: Calibrate High-Dimensional Cox Models
> ### Aliases: hdnom.calibrate
> 
> ### ** Examples
> 
> library("survival")
> 
> # Load imputed SMART data
> data("smart")
> x = as.matrix(smart[, -c(1, 2)])
> time = smart$TEVENT
> event = smart$EVENT
> y = Surv(time, event)
> 
> # Fit Cox model with lasso penalty
> fit = hdcox.lasso(x, y, nfolds = 5, rule = "lambda.1se", seed = 11)
> 
> # Model calibration by fitting the original data directly
> cal.fitting = hdnom.calibrate(
+   x, time, event, model.type = "lasso",
+   alpha = 1, lambda = fit$lasso_best_lambda,
+   method = "fitting",
+   pred.at = 365 * 9, ngroup = 5,
+   seed = 1010)
Start fitting ...
> 
> # Model calibration by 5-fold cross-validation
> cal.cv = hdnom.calibrate(
+   x, time, event, model.type = "lasso",
+   alpha = 1, lambda = fit$lasso_best_lambda,
+   method = "cv", nfolds = 5,
+   pred.at = 365 * 9, ngroup = 5,
+   seed = 1010)
Start fold 1 
Start fold 2 
Start fold 3 
Start fold 4 
Start fold 5 
> 
> print(cal.fitting)
High-Dimensional Cox Model Calibration Object
Random seed: 1010 
Calibration method: fitting
Model type: lasso 
glmnet model alpha: 1 
glmnet model lambda: 0.0235179 
glmnet model penalty factor: not specified
Calibration time point: 3285 
Number of groups formed for calibration: 5 
> summary(cal.fitting)
  Calibration Summary Table
  Predicted  Observed Lower 95% Upper 95%
1 0.6084404 0.4670959 0.3931194 0.5549932
2 0.7010189 0.6906300 0.5617393 0.8490947
3 0.7455827 0.8047966 0.7566516 0.8560051
4 0.7790308 0.8132201 0.7256294 0.9113837
5 0.8169391 0.8988891 0.8646299 0.9345058
> plot(cal.fitting)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Quitting from lines 193-194 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hdnom.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hdrscatterplot
> ### Title: Scatterplot showing bivariate highest density regions
> ### Aliases: hdrscatterplot
> ### Keywords: distribution hplot smooth
> 
> ### ** Examples
> 
> 
> x <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
> y <- c(rnorm(200, 0, 1), rnorm(200, 4, 1))
> hdrscatterplot(x, y)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘healthcareai-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: control_chart
> ### Title: Create a control chart
> ### Aliases: control_chart
> 
> ### ** Examples
> 
> d <-
+   tibble::data_frame(
+     day = sample(c("Monday", "Tuesday", "Wednesday", "Thursday", "Friday"),
+                  100, TRUE),
+     person = sample(c("Tom", "Jane", "Alex"), 100, TRUE),
+     count = rbinom(100, 20, ifelse(day == "Friday", .5, .2)),
+     date = Sys.Date() - sample.int(100))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> 
> # Minimal arguments are the data and the column to put on the y-axis.
> # If x is not provided, observations will be plotted in order of the rows
> 
> control_chart(d, "count")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: control_chart ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 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:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘heatmaply.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: block_average
> ### Title: Calculate yearly means for event metrics.
> ### Aliases: block_average
> 
> ### ** Examples
> 
> ts <- ts2clm(sst_WA, climatologyPeriod = c("1983-01-01", "2012-12-31"))
> res <- detect_event(ts)
> out <- block_average(res)
> summary(glm(count ~ year, out, family = "poisson"))

Call:
glm(formula = count ~ year, family = "poisson", data = out)

Deviance Residuals: 
    Min       1Q   Median       3Q      Max  
-2.3992  -1.5279  -0.5768   0.6122   3.7773  

Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
(Intercept) -105.58986   29.22236  -3.613 0.000302 ***
year           0.05308    0.01459   3.638 0.000275 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 89.964  on 32  degrees of freedom
Residual deviance: 75.723  on 31  degrees of freedom
AIC: 133.7

Number of Fisher Scoring iterations: 6

> 
> library(ggplot2)
> 
> ggplot(data = out, aes(x = year, y = count)) +
+   geom_point(colour = "salmon") +
+   geom_line() +
+   labs(x = NULL, y = "Number of events")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: run_dsa
> ### Title: Run Sensitivity Analysis
> ### Aliases: run_dsa
> 
> ### ** Examples
> 
> param <- define_parameters(
+   p1 = .5,
+   p2 = .2,
+   r = .05
+ )
> mod1 <- define_strategy(
+   transition = define_transition(
+     C, p1,
+     p2, C
+   ),
+   define_state(
+     cost = discount(543, r),
+     ly = 1
+   ),
+   define_state(
+     cost = discount(432, r),
+     ly = .5
+   )
+ )
No named state -> generating names.
No named state -> generating names.
> 
> mod2 <- define_strategy(
+   transition = define_transition(
+     C, p1,
+     p2, C
+   ),
+   define_state(
+     cost = 789,
+     ly = 1
+   ),
+   define_state(
+     cost = 456,
+     ly = .8
+   )
+ )
No named state -> generating names.
No named state -> generating names.
> 
> res2 <- run_model(
+   mod1, mod2,
+   parameters = param,
+   init = c(100, 0),
+   cycles = 10,
+   cost = cost,
+   effect = ly
+ )
No named model -> generating names.
> 
> ds <- define_dsa(
+   p1, .1, .9,
+   p2, .1, .3,
+   r, .05, .1
+ )
> print(ds)
   Low  High
p1 0.1  0.9 
p2 0.1  0.3 
r  0.05 0.1 
> 
> x <- run_dsa(res2, ds)
Running DSA on strategy 'I'...
Running DSA on strategy 'II'...
> 
> plot(x, value = "cost")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [54s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(heemod)
  > 
  > ## the Sys.setenv fixes a problem running tests
  > ##   with parallel processing; related to
  > ##   https://github.com/hadley/testthat/issues/86 and
  > ##   https://github.com/hadley/testthat/issues/144
  > 
  > Sys.setenv("R_TESTS" = "")
  > test_check("heemod")
  ── 1. Error: Running model from files works. (@test_tabular_input.R#772)  ──────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: run_model_tabular(location = file.path(tempdir(), "tabular", "thr"), run_psa = TRUE, 
         run_demo = TRUE, save = TRUE, overwrite = TRUE) at testthat/test_tabular_input.R:772
  2: save_outputs(outputs, output_dir, overwrite)
  3: save_graph(this_plot, output_dir, this_file)
  4: print(plot)
  5: print.ggplot(plot)
  6: ggplot_gtable(data)
  7: ggplot_gtable.ggplot_built(data)
  8: layout$render(geom_grobs, data, theme, plot$labels)
  9: f(..., self = self)
  10: self$facet$draw_panels(panels, self$layout, self$panel_scales_x, self$panel_scales_y, 
         self$panel_params, self$coord, data, theme, self$facet_params)
  11: f(...)
  12: render_strips(col_vars, row_vars, params$labeller, theme)
  13: build_strip(y, labeller, theme, FALSE)
  14: ggstrip(grobs_right, theme, element, gp, horizontal, clip = "on")
  15: Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin", "unit")), na.rm = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 471 SKIPPED: 0 FAILED: 1
  1. Error: Running model from files works. (@test_tabular_input.R#772) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘helixvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_wenxiang
> ### Title: Create Wenxiang diagrams to visualize alpha helical sequences.
> ### Aliases: draw_wenxiang
> 
> ### ** Examples
> 
> draw_wenxiang("GIGAVLKVLTTGLPALIS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 52-57 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ctstm.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 189-206 (ctstm.Rmd) 
Error: processing vignette 'ctstm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ctstm.Rmd’

--- re-building ‘icea.Rmd’ using rmarkdown
Quitting from lines 169-177 (icea.Rmd) 
Error: processing vignette 'icea.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘icea.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 262-269 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘psm.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 179-198 (psm.Rmd) 
Error: processing vignette 'psm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘psm.Rmd’

SUMMARY: processing the following files failed:
  ‘ctstm.Rmd’ ‘icea.Rmd’ ‘intro.Rmd’ ‘psm.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘detect_idiosyncratic_vignette.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 59-68 (detect_idiosyncratic_vignette.Rmd) 
Error: processing vignette 'detect_idiosyncratic_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘detect_idiosyncratic_vignette.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
--- finished re-building ‘README.Rmd’

--- re-building ‘confusion-matrix.Rmd’ using rmarkdown
--- finished re-building ‘confusion-matrix.Rmd’

--- re-building ‘cross-validation.Rmd’ using rmarkdown
Quitting from lines 96-105 (cross-validation.Rmd) 
Error: processing vignette 'cross-validation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cross-validation.Rmd’

--- re-building ‘how-to-make-heuristic.Rmd’ using rmarkdown
--- finished re-building ‘how-to-make-heuristic.Rmd’

--- re-building ‘reproducing-results.Rmd’ using rmarkdown
--- finished re-building ‘reproducing-results.Rmd’

SUMMARY: processing the following file failed:
  ‘cross-validation.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorRamps
> ### Title: Color Ramps on Perceptually Linear Scales
> ### Aliases: ColorRamps LinGray BTC BTY LinOCS heat.ob magent plinrain
> ### Keywords: color
> 
> ### ** Examples
> 
> h <- hexbin(rnorm(10000),rnorm(10000))
> plot(h, colramp= BTY)
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")
Calls: plot -> plot -> .local -> hexViewport -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hexagon_binning.Rnw’ using Sweave

Error: processing vignette 'hexagon_binning.Rnw' failed with diagnostics:
 chunk 1 (label = comphexsq) 
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")

--- failed re-building ‘hexagon_binning.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sticker
> ### Title: sticker
> ### Aliases: sticker
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(aes(x = mpg, y = wt), data = mtcars) + geom_point()
> p <- p + theme_void() + theme_transparent()
> sticker(p, package="hexSticker")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sticker ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘hhi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_hhi
> ### Title: Plots a Herfindahl-Hirschman Index Time Series
> ### Aliases: plot_hhi
> 
> ### ** Examples
> 
> hhi <- c(45,60,50,100,94,15,88,200,215,68,
+ 47,62,52,102,96,17,90,202,217,70)
> year <- c(1990,1991,1992,1993,1994,1995,1996,1997,1998,1999,
+ 2000,2001,2002,2003,2004,2005,2006,2007,2008,2009)
> data <- data.frame(hhi, year)
> plot_hhi(data, "year", "hhi")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HH-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hovBF
> ### Title: Homogeneity of Variance: Brown-Forsyth method
> ### Aliases: hovBF hovplotBF
> ### Keywords: dplot
> 
> ### ** Examples
> 
> data(batch)
> batch1.aov <- aov(Calcium ~ Batch, data=batch)
> anova(batch1.aov)
Analysis of Variance Table

Response: Calcium
          Df   Sum Sq  Mean Sq F value   Pr(>F)   
Batch      4 0.096976 0.024244  5.5352 0.003626 **
Residuals 20 0.087600 0.004380                    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
> hovBF(Calcium ~ Batch, data=batch)

	hov: Brown-Forsyth

data:  Calcium
F = 0.032193, df:Batch = 4, df:Residuals = 20, p-value = 0.9978
alternative hypothesis: variances are not identical

> hovplotBF(Calcium ~ Batch, data=batch)
Warning in formals(fun) : argument is not a function
Warning in formals(fun) : argument is not a function
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: <Anonymous> ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Running examples in ‘hierarchicalSets-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_outlier_distribution
> ### Title: Plot the outlying elements of a HierarchicalSet object
> ### Aliases: plot_outlier_distribution
> 
> ### ** Examples
> 
> data('twitter')
> 
> twitSet <- create_hierarchy(twitter)
> plot_outlier_distribution(twitSet)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HierDpart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DeltaDcorplot
> ### Title: Plot correlation matrix for pairwise Delta D
> ### Aliases: DeltaDcorplot
> ### Keywords: Correlation plot Plot genetic differentiation
> 
> ### ** Examples
> 
> # example genepop file
> f <- system.file('extdata',package='HierDpart')
> infile <- file.path(f, "Island.gen")
> DeltaDcorplot(infile,ncode=3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HierDpart.Rmd’ using rmarkdown
Quitting from lines 59-60 (HierDpart.Rmd) 
Error: processing vignette 'HierDpart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘HierDpart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Running examples in ‘HighDimOut-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Func.ABOD
> ### Title: Angle-based outlier detection (ABOD) algorithm
> ### Aliases: Func.ABOD
> 
> ### ** Examples
> 
> library(ggplot2)
> res.ABOD <- Func.ABOD(data=TestData[,1:2], basic=FALSE, perc=0.2)
Warning: executing %dopar% sequentially: no parallel backend registered
> data.temp <- TestData[,1:2]
> data.temp$Ind <- NA
> data.temp[order(res.ABOD, decreasing = FALSE)[1:10],"Ind"] <- "Outlier"
> data.temp[is.na(data.temp$Ind),"Ind"] <- "Inlier"
> data.temp$Ind <- factor(data.temp$Ind)
> ggplot(data = data.temp) + geom_point(aes(x = x, y = y, color=Ind, shape=Ind))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘hIRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: latent_scores
> ### Title: Estimates of Latent Preferences/Abilities
> ### Aliases: latent_scores
> 
> ### ** Examples
> 
> y <- nes_econ2008[, -(1:3)]
> x <- model.matrix( ~ party * educ, nes_econ2008)
> z <- model.matrix( ~ party, nes_econ2008)
> nes_m1 <- hgrm(y, x, z)
...................
 converged at iteration 19 
> pref <- latent_scores(nes_m1)
> require(ggplot2)
Loading required package: ggplot2
> ggplot(data = nes_econ2008) +
+ geom_density(aes(x = pref$est, col = party))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages-- use center alignment (requires width=ODD)
> require(gtools, warn.conflicts=FALSE)
Loading required package: gtools
> mav3<-running(Bowley$Value, width=3, align="center")
> mav5<-running(Bowley$Value, width=5, align="center")
> mav9<-running(Bowley$Value, width=9, align="center")
> lines(Bowley$Year[2:44], mav3, col='blue', lty=2)
> lines(Bowley$Year[3:43], mav5, col='green3', lty=3)
> lines(Bowley$Year[5:41], mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> require(ggplot2, warn.conflicts=FALSE)
Loading required package: ggplot2
> qplot(Year,Value, data=Bowley)+geom_smooth()
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HistDAWass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data2hist
> ### Title: From real data to distributionH.
> ### Aliases: data2hist
> 
> ### ** Examples
> 
> data=rnorm(n = 1000,mean = 2,sd = 3)
> mydist=data2hist(data)
> plot(mydist)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘historydata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: early_colleges
> ### Title: Early colleges in the United States
> ### Aliases: early_colleges
> ### Keywords: datasets
> 
> ### ** Examples
> 
> head(early_colleges)
                 college         original_name         city state established
1                Harvard                  <NA>    Cambridge    MA        1636
2       William and Mary                  <NA> Williamsburg    VA        1693
3                   Yale                  <NA>    New Haven    CT        1701
4 Pennsylvania, Univ. of                  <NA> Philadelphia    PA        1740
5              Princeton College of New Jersey    Princeton    NJ        1746
6               Columbia        King's College     New York    NY        1754
                           sponsorship
1 Congregational; after 1805 Unitarian
2                             Anglican
3                       Congregational
4                    Nondenominational
5                         Presbyterian
6                             Anglican
> if(require(ggplot2)) {
+   ggplot(early_colleges, aes(x = established)) + geom_bar(binwidth = 5) +
+   ggtitle("Founding Dates of Early American Colleges")
+ }
Loading required package: ggplot2
Warning: `geom_bar()` no longer has a `binwidth` parameter. Please use `geom_histogram()` instead.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HLMdiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_eb_ls
> ### Title: Visually comparing shrinkage and LS estimates
> ### Aliases: compare_eb_ls
> 
> ### ** Examples
> 
> library(lme4)
Loading required package: Matrix
> wages.fm1 <- lmer(lnw ~ exper + (exper | id), data = wages)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00609024 (tol = 0.002, component 1)
> wages.sepLM <- adjust_lmList(lnw ~ exper | id, data = wages)
> rancoef.eb <- coef(wages.fm1)$id
> rancoef.ols <- coef(wages.sepLM) # note diff. length than rancoef.eb
> compare_eb_ls(eb = rancoef.eb[rownames(rancoef.ols),], ols = rancoef.ols, identify = 0.01)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: compare_eb_ls ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Hmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggfreqScatter
> ### Title: Frequency Scatterplot
> ### Aliases: ggfreqScatter
> ### Keywords: hplot
> 
> ### ** Examples
> 
> set.seed(1)
> x <- rnorm(1000)
> y <- rnorm(1000)
> count <- sample(1:100, 1000, TRUE)
> x <- rep(x, count)
> y <- rep(y, count)
> # color=alpha=NULL below makes loess smooth over all points
> g <- ggfreqScatter(x, y) +   # might add g=0 if using plotly
+       geom_smooth(aes(color=NULL, alpha=NULL), se=FALSE) +
+       ggtitle("Using Deciles of Frequency Counts, 2500 Bins")
> g
Warning: Using alpha for a discrete variable is not advised.
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘HoRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: regressogram
> ### Title: Regressogram
> ### Aliases: regressogram
> ### Keywords: file
> 
> ### ** Examples
>  
> ## Regressogram for the natural gas dataset.
> 
> data(gas)
> 
> regressogram(x = gas$LA, y = gas$OK, nbins = 6, x.lab = "LA",
+              y.lab = "OK", main = "Regressogram")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘hpiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.hpi
> ### Title: Plot method for 'hpi' object
> ### Aliases: plot.hpi
> 
> ### ** Examples
> 
> 
>  # Load data
>  data(ex_sales)
> 
>  # Create index with raw transaction data
>  rt_index <- rtIndex(trans_df = ex_sales,
+                      periodicity = 'monthly',
+                      min_date = '2010-06-01',
+                      max_date = '2015-11-30',
+                      adj_type = 'clip',
+                      date = 'sale_date',
+                      price = 'sale_price',
+                      trans_id = 'sale_id',
+                      prop_id = 'pinx',
+                      estimator = 'robust',
+                      log_dep = TRUE,
+                      trim_model = TRUE,
+                      max_period = 48,
+                      smooth = FALSE)
Supplied "min_date" date is greater than minimum of transactions. Clipping transactions.

Supplied "max_date" is less than maximum of transactions. Clipping transactions.

> 
>  # Plot data
>  plot(rt_index)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classstructure.Rmd’ using rmarkdown
--- finished re-building ‘classstructure.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 228-230 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_check
> ### Title: Spell check ggplot2 plot labels
> ### Aliases: gg_check
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> df <- data.frame(x=c(20, 25, 30), y=c(4, 4, 4), txt=c("One", "Two", "Three"))
> 
> # not piping
> ggplot(mtcars, aes(mpg, wt)) +
+   geom_point() +
+   labs(x="This is some txt", y="This is more text",
+        title="Thisy is a titlle",
+        subtitle="This is a subtitley",
+        caption="This is a captien") -> gg
> 
> gg_check(gg)
Possible misspelled words in [title]: (Thisy, titlle)
Possible misspelled words in [subtitle]: (subtitley)
Possible misspelled words in [caption]: (captien)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘why_hrbrthemes.Rmd’ using rmarkdown
Quitting from lines 36-51 (why_hrbrthemes.Rmd) 
Error: processing vignette 'why_hrbrthemes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘why_hrbrthemes.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hrm.plot
> ### Title: Plots profiles of the groups in case of one whole- and one
> ###   subplot-factor.
> ### Aliases: hrm.plot
> ### Keywords: internal
> 
> ### ** Examples
> 
> data(EEG)
> head(EEG)
  group    value sex subject variable region dimension
1  SCC+ 2.804180   W       1        1      1         1
2  SCC+ 2.285004   W       1        1      2         2
3  SCC+ 1.473094   W       1        1      3         3
4  SCC+ 1.548939   W       1        1      4         4
5  SCC+ 2.160346   W       1        1      5         5
6  SCC+ 2.143525   W       1        1      6         6
> 
> # plots profiles according to groups with
> # subplot-factor called dimension
> 
> # first create an HRM object
> object_hrm <- hrm_test(value ~ group*dimension, subject = "subject", data = EEG)
> 
> # plot the HRM object, here we use the additional argument 'theme_bw()' for ggplot2
> plot(object_hrm, legend = TRUE, legend.title = "Group", ... =  theme_bw() )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hutils.Rmd’ using rmarkdown
Quitting from lines 396-404 (hutils.Rmd) 
Error: processing vignette 'hutils.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘hutils.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hwx.test
> ### Title: Test for HW by either full enumeration or Monte Carlo.
> ### Aliases: hwx.test
> 
> ### ** Examples
> 
> # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
> c <- c(0,3,1,5,18,1,3,7,5,2)
> hwx.test(c)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
> # To see a histogram of the LLR statistic:
> hwx.test(c, histobins=TRUE)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
Loading required namespace: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘HWxtest.Rmd’ using rmarkdown
Quitting from lines 146-147 (HWxtest.Rmd) 
Error: processing vignette 'HWxtest.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘HWxtest.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_hydroscoper.Rmd’ using rmarkdown
Quitting from lines 115-125 (intro_hydroscoper.Rmd) 
Error: processing vignette 'intro_hydroscoper.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_hydroscoper.Rmd’

--- re-building ‘stations_with_data.Rmd’ using rmarkdown
Quitting from lines 50-61 (stations_with_data.Rmd) 
Error: processing vignette 'stations_with_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stations_with_data.Rmd’

SUMMARY: processing the following files failed:
  ‘intro_hydroscoper.Rmd’ ‘stations_with_data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IAPWS95.Rmd’ using rmarkdown
Quitting from lines 121-144 (IAPWS95.Rmd) 
Error: processing vignette 'IAPWS95.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IAPWS95.Rmd’

SUMMARY: processing the following file failed:
  ‘IAPWS95.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.048 seconds
---------------
IBD analysis finished. Total time used: 0.051 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Running examples in ‘ICtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggladleplot
> ### Title: Ladle Plot for an Object of Class ladle Using ggplot2
> ### Aliases: ggladleplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> n <- 1000
> X <- cbind(rexp(n), rt(n,5), rnorm(n), rnorm(n), rnorm(n), rnorm(n))
> test <- FOBIladle(X)
> ggladleplot(test)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ICA.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
--- finished re-building ‘ICA.Rmd’

--- re-building ‘PCA.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
Quitting from lines 66-71 (PCA.Rmd) 
Error: processing vignette 'PCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PCA.Rmd’

--- re-building ‘SIR.Rmd’ using rmarkdown
Loading required package: JADE
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
--- finished re-building ‘SIR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TimeSeries
> ### Title: Graphical exploratory charts
> ### Aliases: TimeSeries
> 
> ### ** Examples
> 
> Example_IDEAM <- system.file("extdata", "Example_IDEAM", package = "ideamdb")
> TimeSeries(Example_IDEAM, station = "LUCERO")
Warning: Removed 33 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: TimeSeries ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 128-130 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 220-244 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pritikin-schmidt.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomPlot
> ### Title: Identifies anomalous individuals and produces longitudinal plots
> ###   without them and with just them
> ### Aliases: anomPlot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(exampleData)
> anomalous <- anomPlot(longi.dat, response="Area.smooth.AGR", 
+                       lower=2.5, start.time=40, 
+                       x = "xDays+35.42857143", vertical.line=29, 
+                       breaks=seq(28, 42, by=2), 
+                       whichPrint=c("innerPlot"), 
+                       y.title="Area.smooth.AGR")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: anomPlot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    convolve, spectrum

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

    frame

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

    save.image


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 152-158 (gettingstarted.Rmd) 
Error: processing vignette 'gettingstarted.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gettingstarted.Rmd’

--- re-building ‘pixsets.Rmd’ using rmarkdown
Loading required package: magrittr

Attaching package: 'imager'

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

    add

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

    convolve, spectrum

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

    frame

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

    save.image


Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotComparison
> ### Title: Plots comparison between the original and the new balanced
> ###   dataset.
> ### Aliases: plotComparison
> 
> ### ** Examples
> 
> data(iris0)
> set.seed(12345)
> 
> rwoSamples <- rwo(iris0, numInstances = 100)
> rwoBalanced <- rbind(iris0, rwoSamples)
> plotComparison(iris0, rwoBalanced, names(iris0), cols = 2, classAttr = "Class")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotComparison ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘imbalance.Rmd’ using rmarkdown
Quitting from lines 70-75 (imbalance.Rmd) 
Error: processing vignette 'imbalance.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘imbalance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 73-76 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘parallel.Rmd’ using rmarkdown
Quitting from lines 51-53 (parallel.Rmd) 
Error: processing vignette 'parallel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘parallel.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘parallel.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_errors
> ### Title: Function to plot the Error Comparison
> ### Aliases: plot_errors plot_errors.errprof
> 
> ### ** Examples
> 
> aa <- impute_errors(dataIn = nottem)
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
Warning in predict.lm(fit, newdata = data.frame(X)) :
  prediction from a rank-deficient fit may be misleading
> 
> # default plot
> plot_errors(aa)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘imsig-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_abundance
> ### Title: Plot relative abundance of immune cells
> ### Aliases: plot_abundance
> 
> ### ** Examples
> 
> plot_abundance (exp = example_data, r = 0.7)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_abundance ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘IncDTW-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dtw_partial
> ### Title: Partial Dynamic Time Warping
> ### Aliases: dtw_partial
> ### Keywords: cluster ts
> 
> ### ** Examples
> 
> # open-end alignment for multivariate time series
> # first simulate a 2-dim time series Q
> Q <- matrix(cumsum(rnorm(100)), ncol=2)
> 
> # simulate C as noisy and warped version of Q, and append noise at the end
> C <- Q[sort(sample(50, 40, replace=FALSE)), ] + rnorm(80)
> C <- rbind(C, matrix(rnorm(30), ncol=2))
> 
> tmp <- dtw(Q = Q, C = C, ws = 30, return_QC = TRUE, return_wp = TRUE)
> par <- dtw_partial(tmp, partial_C = TRUE)
> par
$rangeQ
[1]  1 50

$rangeC
[1]  1 38

$normalized_distance
[1] 1.344722

> plot(tmp, partial = par, type = "QC")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Incremental_Dynamic_Time_Warping.Rmd’ using rmarkdown

Attaching package: 'IncDTW'

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

    cm

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

    norm

Loading required package: proxy

Attaching package: 'proxy'

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

    as.dist, dist

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

    as.matrix

Loaded dtw v1.20-1. See ?dtw for help, citation("dtw") for use in publication.


Attaching package: 'dtw'

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

    dtw

Quitting from lines 73-74 (Incremental_Dynamic_Time_Warping.Rmd) 
Error: processing vignette 'Incremental_Dynamic_Time_Warping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Incremental_Dynamic_Time_Warping.Rmd’

--- re-building ‘Runtime_Comparison.Rmd’ using rmarkdown
Quitting from lines 102-108 (Runtime_Comparison.Rmd) 
Error: processing vignette 'Runtime_Comparison.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Runtime_Comparison.Rmd’

SUMMARY: processing the following files failed:
  ‘Incremental_Dynamic_Time_Warping.Rmd’ ‘Runtime_Comparison.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Bootstrap incidence time series
> ### Aliases: bootstrap
> 
> ### ** Examples
> 
> 
> if (require(outbreaks) && require(ggplot2)) { withAutoprint({
+   i <- incidence(fluH7N9_china_2013$date_of_onset)
+   i
+   plot(i)
+ 
+   ## one simple bootstrap
+   x <- bootstrap(i)
+   x
+   plot(x)
+ 
+ })}
Loading required package: outbreaks
Loading required package: ggplot2
> i <- incidence(fluH7N9_china_2013$date_of_onset)
10 missing observations were removed.
> i
<incidence object>
[126 cases from days 2013-02-19 to 2013-07-27]

$counts: matrix with 159 rows and 1 columns
$n: 126 cases in total
$dates: 159 dates marking the left-side of bins
$interval: 1 day
$timespan: 159 days
$cumulative: FALSE

> plot(i)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: withAutoprint ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘conversions.Rmd’ using rmarkdown
Quitting from lines 49-55 (conversions.Rmd) 
Error: processing vignette 'conversions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘conversions.Rmd’

--- re-building ‘customize_plot.Rmd’ using rmarkdown
Quitting from lines 78-81 (customize_plot.Rmd) 
Error: processing vignette 'customize_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customize_plot.Rmd’

--- re-building ‘incidence_class.Rmd’ using rmarkdown
Quitting from lines 47-50 (incidence_class.Rmd) 
Error: processing vignette 'incidence_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incidence_class.Rmd’

--- re-building ‘incidence_fit_class.Rmd’ using rmarkdown
Quitting from lines 55-63 (incidence_fit_class.Rmd) 
Error: processing vignette 'incidence_fit_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incidence_fit_class.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 132-135 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following files failed:
  ‘conversions.Rmd’ ‘customize_plot.Rmd’ ‘incidence_class.Rmd’
  ‘incidence_fit_class.Rmd’ ‘overview.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: incRplot
> ### Title: Quick visualisation of incubation temperatures, on-bouts and
> ###   off-bouts
> ### Aliases: incRplot
> 
> ### ** Examples
> 
> # loading example data
> data(incR_procdata)
> my_plot <- incRplot(data = incR_procdata[complete.cases(incR_procdata$temperature),], 
+                     time.var = "dec_time", 
+                     day.var = "date", 
+                     inc.temperature.var = "temperature", 
+                     env.temperature.var = "env_temp",
+                     vector.incubation = "incR_score")
>                     
> # see your plot
> my_plot
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘incR_pipeline.Rmd’ using rmarkdown
Quitting from lines 116-125 (incR_pipeline.Rmd) 
Error: processing vignette 'incR_pipeline.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘incR_pipeline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EstimatingIncidence.Rmd’ using rmarkdown
--- finished re-building ‘EstimatingIncidence.Rmd’

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

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

--- re-building ‘TestCalibration.Rmd’ using rmarkdown
Quitting from lines 96-97 (TestCalibration.Rmd) 
Error: processing vignette 'TestCalibration.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TestCalibration.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateCutTimeForGrowthCurve
> ### Title: calculateCutTimeForGrowthCurve
> ### Aliases: calculateCutTimeForGrowthCurve
> 
> ### ** Examples
> 
> pm_file <- system.file(file='extdata/example.PlateMap', package='IncucyteDRC')
> test_pm <- importPlatemapXML(pm_file)
Importing platemap xml from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example.PlateMap
Plate map import successful!
> data_file <- system.file(file='extdata/example_data.txt', package='IncucyteDRC')
> test_data <- importIncucyteData(data_file, metric='pc')
Getting pc data for plate example_data.txt from:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/IncucyteDRC/extdata/example_data.txt
> 
> test_list <- splitIncucyteDRCPlateData(test_pm, test_data, group_columns='growthcondition')
> 
> print(test_list)
## This is an IncucyteDRCSetList S3 object containing 4 IncucyteDRCSet objects
## Access using standard list notation ie my_list[[1]]
## Try lapply(my_list, print) to see more information on each object> 
> test_idrc_set <- fitGrowthCurvesGrouped(test_list[[2]])
> plotIncucyteDRCSet(test_idrc_set, grouped=TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IncucyteZoomExport.Rmd’ using rmarkdown
--- finished re-building ‘IncucyteZoomExport.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Quitting from lines 35-36 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_clust_sc
> ### Title: Dendrogram of the cluster analysis.
> ### Aliases: plot_clust_sc
> 
> ### ** Examples
> 
> # Using the Baltic Sea demo data
> scores_tbl <- scoring(trend_tbl = model_trend_ex,
+   mod_tbl = all_results_ex, press_type = press_type_ex)
> scores_mat <- summary_sc(scores_tbl)$scores_matrix
> dist_matrix <- dist_sc(scores_mat, method_dist = "euclidean")
> clust_analysis <- clust_sc(dist_matrix, method_clust = "complete")
With the selected agglomeration method (complete), the cophonetic correlation coeffient is 0.842 and the Gower distance is 417.41.
> plot_clust_sc(clust_analysis)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘iNextPD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggiNEXT
> ### Title: ggplot2 extension for an iNextPD object
> ### Aliases: ggiNEXT ggiNEXT.default ggiNEXT.iNextPD
> 
> ### ** Examples
> 
> # single-assemblage abundance data
> data(bird)
> bird.phy <- ade4::newick2phylog(bird$tre)
> bird.lab <- rownames(bird$abun)
> out1 <- iNextPD(bird$abun$North.site, bird.lab, bird.phy, 
+         q=1, datatype="abundance", endpoint=400, se=TRUE)
> ggiNEXT(x=out1, type=1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown

Attaching package: 'iNextPD'

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

    ggiNEXT

Quitting from lines 294-297 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bird
> ### Title: Bird abundance-based data
> ### Aliases: bird
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> data(bird)
> out <- iNEXT(bird, datatype="abundance")
> ggiNEXT(out)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 253-255 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘Information-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Information
> ### Title: Data exploration with information theory (weight-of-evidence and
> ###   information value)
> ### Aliases: Information Information-package
> ### Keywords: IV, NIV, NWOE, WOE, classification, uplift
> ###   weight-of-evidence,
> 
> ### ** Examples
> 
> ##------------------------------------------------------------
> ## WOE analysis, no validation
> ##------------------------------------------------------------
> library(Information)
> 
> data(train, package="Information")
> train <- subset(train, TREATMENT==1)
> IV <- Information::create_infotables(data=train, y="PURCHASE", parallel=FALSE)
[1] "Variable TREATMENT was removed because it has only 1 unique level"
> 
> print(head(IV$Summary), row.names=FALSE)
                    Variable        IV
             N_OPEN_REV_ACTS 1.0107695
        TOT_HI_CRDT_CRDT_LMT 0.9345902
        RATIO_BAL_TO_HI_CRDT 0.8232539
 D_NA_M_SNC_MST_RCNT_ACT_OPN 0.6355466
  M_SNC_OLDST_RETAIL_ACT_OPN 0.5573438
      M_SNC_MST_RCNT_ACT_OPN 0.5026402
> print(IV$Tables$N_OPEN_REV_ACTS, row.names=FALSE)
 N_OPEN_REV_ACTS    N    Percent        WOE        IV
           [0,0] 1469 0.29545455 -2.0465968 0.6401443
           [1,2]  958 0.19267900 -0.5900120 0.6958705
           [3,3]  310 0.06234916  0.2033085 0.6986029
           [4,5]  583 0.11725664  0.4419768 0.7244762
           [6,8]  632 0.12711183  0.6148243 0.7810611
          [9,11]  453 0.09111022  0.8815772 0.8692672
         [12,48]  567 0.11403862  0.9883818 1.0107695
> 
> # Plotting a single variable
> Information::plot_infotables(IV, "N_OPEN_REV_ACTS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Information-vignette.Rmd’ using rmarkdown_notangle
Quitting from lines 223-224 (Information-vignette.Rmd) 
Error: processing vignette 'Information-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Information-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ks_plot
> ### Title: ks_plot
> ### Aliases: ks_plot
> 
> ### ** Examples
> 
> data('ActualsAndScores')
> ks_plot(actuals=ActualsAndScores$Actuals, predictedScores=ActualsAndScores$PredictedScores)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ks_plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘InformationValue.Rmd’ using rmarkdown
Quitting from lines 65-67 (InformationValue.Rmd) 
Error: processing vignette 'InformationValue.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘InformationValue.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg
> ### Title: ggplot2 geomes for inlabru related objects
> ### Aliases: gg
> 
> ### ** Examples
> 
> 
> # Load Gorilla data
> 
> data(gorillas, package = "inlabru")
> 
> # Invoke ggplot and add geomes for the Gorilla nests and the survey boundary
> 
> ggplot() + gg(gorillas$boundary) + gg(gorillas$nests)
Regions defined for each Polygons
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘insurancerating-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.insurancerating
> ### Title: Automatically create a ggplot for objects obtained from
> ###   construct_tariff_classes()
> ### Aliases: autoplot.insurancerating
> 
> ### ** Examples
> 
> library(ggplot2)
> x <- construct_tariff_classes(MTPL, nclaims, age_policyholder, exposure)
> autoplot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘IntegratedMRF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CombPredict
> ### Title: Integrated Prediction of Testing samples using Combination
> ###   Weights from integrated RF or MRF model
> ### Aliases: CombPredict
> 
> ### ** Examples
> 
> library(IntegratedMRF)
> data(Dream_Dataset)
> Tree=1
> Feature=1
> Leaf=10
> Confidence=80
> finalX=Dream_Dataset[[1]]
> Cell=Dream_Dataset[[2]]
> Y_train_Dream=Dream_Dataset[[3]]
> Y_train_cell=Dream_Dataset[[4]]
> Y_test=Dream_Dataset[[5]]
> Y_test_cell=Dream_Dataset[[6]]
> Drug=1
> Y_train_Drug=matrix(Y_train_Dream[,Drug],ncol=length(Drug))
> Result=Combination(finalX,Y_train_Drug,Cell,Y_train_cell,Tree,Feature,Leaf,Confidence)
Warning in stats::cor(final_genome_BSP1 %*% BSP_temp_coeff1, finalY_bsp_pred[,  :
  the standard deviation is zero
Warning in stats::cor(final_genome_BSP1 %*% BSP_temp_coeff1, finalY_bsp_pred[,  :
  the standard deviation is zero
Elapsed Time for Bootstrap Error Estimation is 0.544
Elapsed Time for Resubstitution Error Estimation is 0.03
Elapsed Time for 0.632+ Bootstrap Error Estimation is 0.0109999999999999
Elapsed Time for Jackknife Confidence Interval Calculation is 0.004
Elapsed Time for Leave-one-out Error Estimation is 0.201
Elapsed Time for N-fold cross validation Error Estimation is 0.097
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Combination ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘interactions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cat_plot
> ### Title: Plot interaction effects between categorical predictors.
> ### Aliases: cat_plot
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> fit <- lm(price ~ cut * color, data = diamonds)
> cat_plot(fit, pred = color, modx = cut, interval = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘categorical.Rmd’ using rmarkdown
Quitting from lines 70-71 (categorical.Rmd) 
Error: processing vignette 'categorical.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘categorical.Rmd’

--- re-building ‘interactions.Rmd’ using rmarkdown
Quitting from lines 56-57 (interactions.Rmd) 
Error: processing vignette 'interactions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interactions.Rmd’

SUMMARY: processing the following files failed:
  ‘categorical.Rmd’ ‘interactions.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inter.binning
> ### Title: The Binning Estimator
> ### Aliases: inter.binning
> ### Keywords: graphics
> 
> ### ** Examples
> 
> library(interflex)
> data(interflex)
> inter.binning(Y = "Y", D = "D", X = "X", Z = "Z1",
+                   data = s1, nbins = 3, vartype = "homoscedastic",
+                   Ylabel = "Y", Dlabel = "Tr", Xlabel="X")
$est.binning
                     x0    coef     se CI_lower CI_upper
X: [-0.396,2.48] 2.0467 -3.0545 0.5001  -4.0411  -2.0679
X: (2.48,3.42]   2.9599  0.5706 0.4823  -0.3808   1.5220
X: (3.42,6.2]    4.1025  3.1651 0.4770   2.2242   4.1061

$binary.treatment
[1] 1

$bin.size
    1     2     3 
0.335 0.330 0.335 

$treat.variation.byGroup
[1] 1.0459 1.2955 0.9281

$X.Lkurtosis
[1] 0.1241

$correctOrder
[1] TRUE

$p.twosided
p.1v2 p.2v3 p.1v3 
0e+00 2e-04 0e+00 

$p.wald
[1] 0.5054

$graph
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘interplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: interplot
> ### Title: Plot Conditional Coefficients of a Variable in an Interaction
> ###   Term
> ### Aliases: interplot
> 
> ### ** Examples
> 
> data(mtcars)
> m_cyl <- lm(mpg ~ wt * cyl, data = mtcars)
> library(interplot)
> 
> # Plot interactions with a continous conditioning variable
> interplot(m = m_cyl, var1 = 'cyl', var2 = 'wt') +
+ xlab('Automobile Weight (thousands lbs)') +
+ ylab('Estimated Coefficient for Number of Cylinders') +
+ ggtitle('Estimated Coefficient of Engine Cylinders\non Mileage by Automobile Weight') +
+ theme(plot.title = element_text(face='bold'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘interplot-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: abind
Loading required package: arm
Loading required package: MASS
Loading required package: Matrix
Loading required package: lme4

arm (Version 1.10-1, built: 2018-4-12)

Working directory is /home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/interplot.Rcheck/vign_test/interplot/vignettes

Quitting from lines 78-81 (interplot-vignette.Rmd) 
Error: processing vignette 'interplot-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interplot-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConsensusMatPlot
> ### Title: A function to create image plot of the consensus matrix
> ### Aliases: ConsensusMatPlot
> 
> ### ** Examples
> 
> prop <- c(0.20,0.30,0.27,0.23)
> effect <- 2.5
> sim.D <- InterSIM(n.sample=100,cluster.sample.prop=prop,delta.methyl=effect,
+ delta.expr=effect,delta.protein=effect,p.DMP=0.25,p.DEG=NULL,p.DEP=NULL,
+ do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)
> dat1 <- sim.D$dat.methyl
> dat2 <- sim.D$dat.expr
> dat3 <- sim.D$dat.protein
> true.cluster.assignment <- sim.D$clustering.assignment
> 
> ## Make all data positive by shifting to positive direction.
> ## Also rescale the datasets so that they are comparable.
> if (!all(dat1>=0)) dat1 <- pmax(dat1 + abs(min(dat1)), .Machine$double.eps)
> dat1 <- dat1/max(dat1)
> if (!all(dat2>=0)) dat2 <- pmax(dat2 + abs(min(dat2)), .Machine$double.eps)
> dat2 <- dat2/max(dat2)
> if (!all(dat3>=0)) dat3 <- pmax(dat3 + abs(min(dat3)), .Machine$double.eps)
> dat3 <- dat3/max(dat3)
> 
> # The function nmf.mnnals requires the samples to be on rows and variables on columns.
> dat <- list(dat1,dat2,dat3)
> fit <- nmf.mnnals(dat=dat,k=length(prop),maxiter=200,st.count=20,n.ini=15,ini.nndsvd=TRUE,
+ seed=TRUE)
> ConsensusMatPlot(fit,rowLab=TRUE,colLab=TRUE)
Error in Ops.unit(m, unit(1, "grobwidth", textGrob(coln[i <- which.max(nchar(coln))],  : 
  REAL() can only be applied to a 'numeric', not a 'integer'
Calls: ConsensusMatPlot ... aheatmap -> heatmap_motor -> draw_colnames -> Ops.unit
Execution halted
Running examples in ‘inventorize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ABC
> ### Title: ABC
> ### Aliases: ABC
> 
> ### ** Examples
> 
> ABC(data.frame(SKU= seq(1:1000),demand=runif(1000,1,1000)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ABC ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ipft-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipfPlotEcdf
> ### Title: Plots the cumulative distribution function of the estimated
> ###   error
> ### Aliases: ipfPlotEcdf
> 
> ### ** Examples
> 
> 
>     model <- ipfKnn(ipftrain[, 1:168], ipftrain[, 169:170])
>     estimation <- ipfEstimate(model, ipftest[, 1:168], ipftest[, 169:170])
>     ipfPlotEcdf(estimation)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘IPtoCountry-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IP_plot
> ### Title: Convert IPs to countries and plot on world map
> ### Aliases: IP_plot
> 
> ### ** Examples
> 
> IP_plot(IPs)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘isoband-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iso_to_sfg
> ### Title: Convert isolines or isobands to sfg object
> ### Aliases: iso_to_sfg
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
> library(ggplot2)
> 
> m <- matrix(c(0, 2, 2, 2, 0,
+               0, 1, 0, 1, 0,
+               0, 1, 0, 0, 0,
+               0, 1, 0, 1, 0,
+               0, 0, 0, 0, 0), 5, 5, byrow = TRUE)
> 
> z <- isolines(1:ncol(m), nrow(m):1, m, c(0.5, 1.5))
> lines <- iso_to_sfg(z)
> x <- st_sf(level = names(lines), geometry = st_sfc(lines))
> ggplot(x) + geom_sf(aes(color = level))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘itan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: agi
> ### Title: Analisis grafico de items.
> ### Aliases: agi
> 
> ### ** Examples
> 
> data(datos)
> data(clave)
> respuestas <- subset(datos, select=-id)
> plots <- agi(respuestas, clave, nGrupos=ncol(respuestas)/2)
> plots[[1]][[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ITNr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_degree_distribution
> ### Title: Plot Degree Distribution
> ### Aliases: plot_degree_distribution
> 
> ### ** Examples
> 
> require(igraph)
Loading required package: igraph

Attaching package: ‘igraph’

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

    %c%, %s%, add.edges, add.vertices, delete.edges, delete.vertices,
    get.edge.attribute, get.edges, get.vertex.attribute, is.bipartite,
    is.directed, list.edge.attributes, list.vertex.attributes,
    set.edge.attribute, set.vertex.attribute

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

    decompose, spectrum

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

    union

> ##Create random International Trade Network (igraph object)
> ITN<-erdos.renyi.game(75,0.05,directed = TRUE)
> 
> ##Plot out degree distribution
> plot_degree_distribution(ITN,"in")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/32]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
REAL() can only be applied to a 'numeric', not a 'integer'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  ── 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  ─────────────────
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘jcolors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_jcolors_contin
> ### Title: continuous jcolors color scales
> ### Aliases: scale_color_jcolors_contin scale_colour_jcolors_contin
> ###   scale_fill_jcolors_contin scale_color_jcolors scale_colour_jcolors
> ###   scale_fill_jcolors
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> plt <- ggplot(data.frame(x = rnorm(10000), y = rexp(10000, 1.5)), aes(x = x, y = y)) +
+    geom_hex() + coord_fixed()
> 
> plt + scale_fill_jcolors_contin() + theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_the_jcolors_package.Rmd’ using rmarkdown
Quitting from lines 62-96 (using_the_jcolors_package.Rmd) 
Error: processing vignette 'using_the_jcolors_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_the_jcolors_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘joineRmeta.Rmd’ using rmarkdown
Quitting from lines 227-229 (joineRmeta.Rmd) 
Error: processing vignette 'joineRmeta.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘joineRmeta.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densplot
> ### Title: Plot posterior density from JointAI model
> ### Aliases: densplot densplot.mcmc.list densplot.JointAI
> 
> ### ** Examples
> 
> 
> # fit a JointAI object:
> mod <- lm_imp(y ~ C1 + C2 + M2, data = wideDF, n.iter = 100)
This is new software. Please report any bugs to the package maintainer.
> 
> # Example 1: basic densityplot
> densplot(mod)
> 
> 
> # Example 2: use vlines to mark zero
> densplot(mod, col = c("darkred", "darkblue", "darkgreen"),
+          vlines = list(list(v = rep(0, nrow(summary(mod)$stats)),
+                             col = grey(0.8))))
> 
> 
> # Example 3: use vlines to visualize the posterior mean and 2.5% and 97.5% quantiles
> densplot(mod, vlines = list(list(v = summary(mod)$stats[, "Mean"], lty = 1, lwd = 2),
+                             list(v = summary(mod)$stats[, "2.5%"], lty = 2),
+                             list(v = summary(mod)$stats[, "97.5%"], lty = 2)))
> 
> 
> # Example 4: ggplot version
> densplot(mod, use_ggplot = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [97s/104s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jpmesh)
  > 
  > test_check("jpmesh")
  ── 1. Failure: Coarse multiple meshes to large size (@test-fine_separate.R#65)  
  `res` not equal to "4929".
  1/1 mismatches
  x[1]: "4728"
  y[1]: "4929"
  
  ── 2. Failure: Generate random meshcode (@test-rmesh.R#10)  ────────────────────
  `res` not equal to "50304610".
  1/1 mismatches
  x[1]: "64394175"
  y[1]: "50304610"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 176 SKIPPED: 2 FAILED: 2
  1. Failure: Coarse multiple meshes to large size (@test-fine_separate.R#65) 
  2. Failure: Generate random meshcode (@test-rmesh.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘jrt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: info.plot
> ### Title: Plot the information function for a judge or for the entire set
> ###   of judges.
> ### Aliases: info.plot
> 
> ### ** Examples
> 
> 
> # Simulate data with package mirt
> # (6 judges, 300 productions, ordinal ratings from 1 to 5)
> set.seed(123)
> N <- 300
> judges <- 6
> diffs <- t(apply(matrix(runif(judges*4, .4, 5), judges), 1, cumsum))
> d <- -(diffs - rowMeans(diffs)) + stats::rnorm(judges, mean = 0, sd= 1)
> data <- mirt::simdata(matrix(rlnorm(judges,1,0)), d, N,
+ itemtype = 'graded') + 1
> colnames(data) <- paste("Judge_", 1:dim(data)[2], sep = "")
> data <- as.data.frame(data)
> ### --> See mirt documentation for details
> 
> # Fit model
> fit <- jrt(data, irt.model = "PCM")
The possible responses detected are: 1-2-3-4-5

 -== General Summary ==-
- 6 Judges
- 300 Products
- 5 response categories (1-2-3-4-5)
- Mean judgment = 2.977 | SD = 0.862

-== IRT Summary ==-
- Model: Partial Credit Model (Masters, 1982) | doi: 10.1007/BF02296272
- Estimation package: mirt (Chalmers, 2012) | doi: 10.18637/jss.v048.i06
- Estimation algorithm: Expectation-Maximization (EM; Bock & Atkin, 1981) | doi: 10.1007/BF02293801
- Method of factor scoring: Expected A Posteriori (EAP)
- AIC = 4022.957 | AICc = 4027.701 | BIC = 4115.551 | SABIC = 4022.957

-== Model-based reliability ==-
- Empirical reliability | Average in the sample: .889
- Expected reliability | Assumes a Normal(0,1) prior density: .759

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: jrt ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 85-86 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: jskm
> ### Title: Creates a Kaplan-Meier plot for survfit object.
> ### Aliases: jskm
> 
> ### ** Examples
> 
>  library(survival)
>  data(colon)
>  fit <- survfit(Surv(time,status)~rx, data=colon)
>  jskm(fit, timeby=500)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘jskm.Rmd’ using rmarkdown
Quitting from lines 35-45 (jskm.Rmd) 
Error: processing vignette 'jskm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘jskm.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: effect_plot
> ### Title: Plot simple effects in regression models
> ### Aliases: effect_plot
> 
> ### ** Examples
> 
> # Using a fitted lm model
> states <- as.data.frame(state.x77)
> states$HSGrad <- states$`HS Grad`
> fit <- lm(Income ~ HSGrad + Murder,
+   data = states)
> effect_plot(model = fit, pred = Murder)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘effect_plot.Rmd’ using rmarkdown
Quitting from lines 49-50 (effect_plot.Rmd) 
Error: processing vignette 'effect_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘effect_plot.Rmd’

--- re-building ‘summ.Rmd’ using rmarkdown
Loading required package: Matrix
Quitting from lines 250-251 (summ.Rmd) 
Error: processing vignette 'summ.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘summ.Rmd’

--- re-building ‘svycor.Rmd’ using rmarkdown
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

--- finished re-building ‘svycor.Rmd’

SUMMARY: processing the following files failed:
  ‘effect_plot.Rmd’ ‘summ.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TukeyHSDgg
> ### Title: Tukey HSD Plot
> ### Aliases: TukeyHSDgg
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
> ## examples using it with single level data
> ## differences based on an ANOVA and follow up contrasts
> TukeyHSDgg("cyl", "mpg", mtcars)
Warning in TukeyHSDgg("cyl", "mpg", mtcars) :
  x was not a factor, attempting to coerce
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘kaos-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgr
> ### Title: Chaos Game Representation Object
> ### Aliases: cgr
> 
> ### ** Examples
> 
> ###HIV data
> data("HIV")
> 
> ### encoding the sequence
> HIV.cgr = cgr(HIV, res = 100)
> 
> ###plot the sequence
> cgr.plot(HIV.cgr, mode = "points")
> 
> ###plot the FCGR
> cgr.plot(HIV.cgr, mode = "matrix")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘kayadata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_fuel_mix
> ### Title: Plot fuel mix
> ### Aliases: plot_fuel_mix
> 
> ### ** Examples
> 
> usa_fuel <- get_fuel_mix("United States", collapse_renewables = FALSE)
> plot_fuel_mix(usa_fuel)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘policy_analysis.Rmd’ using rmarkdown
Quitting from lines 88-90 (policy_analysis.Rmd) 
Error: processing vignette 'policy_analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘policy_analysis.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hist.kdetrees
> ### Title: Create a histogram of tree density estimates
> ### Aliases: hist.kdetrees
> 
> ### ** Examples
> 
> result <- kdetrees(apicomplexa)
> hist(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kdetrees.Rnw’ using Sweave
Error: processing vignette 'kdetrees.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kdetrees.Rnw’

--- re-building ‘simulation.Rnw’ using Sweave
Loading required package: ade4
Loading required package: lattice
--- finished re-building ‘simulation.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kdtools.Rmd’ using rmarkdown
--- finished re-building ‘kdtools.Rmd’

--- re-building ‘methods.Rmd’ using rmarkdown
Quitting from lines 82-95 (methods.Rmd) 
Error: processing vignette 'methods.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘methods.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: transform_kendall_rw
> ### Title: Transforming (scaling and shifting) Kendall random walks
> ### Aliases: transform_kendall_rw
> 
> ### ** Examples
> 
> kendall_simulations <- simulate_kendall_rw(10, 1000, runif, 0.5)
> scaled_kendall <- transform_kendall_rw(kendall_simulations, (1:1000)^(-2))
> scaled_kendall # kendall random walked scaled by the sequence n^(-1/alpha)
Simulations of Kendall random walk 
Number of simulations:  10 
Length of a single simulation:  1000 
Step distribution:  runif 
Alpha parameter:  0.5> scaled_data <- scaled_kendall$simulation # simulated values
> plot(scaled_kendall)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘behaviour.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 36-38 (behaviour.Rmd) 
Error: processing vignette 'behaviour.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘behaviour.Rmd’

--- re-building ‘kendall_rws.Rmd’ using rmarkdown
Quitting from lines 23-29 (kendall_rws.Rmd) 
Error: processing vignette 'kendall_rws.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kendall_rws.Rmd’

SUMMARY: processing the following files failed:
  ‘behaviour.Rmd’ ‘kendall_rws.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using knitr
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_soil
> ### Title: FAO Soil Reference Groups Colour Scheme for ggplot2
> ### Aliases: scale_colour_soil scale_color_soil scale_fill_soil
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> soil <- data.frame(
+   name = c("Acrisol", "Albeluvisol", "Andosol", "Anthrosol", "Arenosol",
+            "Calcisol", "Cambisol", "Chernozem", "Cryosol", "Fluvisol",
+            "Kastanozem", "Gleysol", "Gypsisol", "Histosol", "Leptosol",
+            "Luvisol", "Phaeozem", "Planosol", "Podzol", "Regosol", "Solonchak",
+            "Solonetz", "Umbrisol", "Vertisol")
+ )
> 
> ggplot(soil, aes(fill = name)) +
+   geom_rect(aes(xmin = rep(0, 24), xmax = rep(1, 24),
+                 ymin = 1:24, ymax = 1:24+1)) +
+   scale_y_reverse() +
+   scale_fill_soil(name = "Soil")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘kmed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barplotnum
> ### Title: Barplot of each cluster for numerical variables data set.
> ### Aliases: barplotnum
> 
> ### ** Examples
> 
> dat <- iris[,1:4]
> memb <- cutree(hclust(dist(dat)),3)
> barplotnum(dat, memb)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kmedoid.Rmd’ using rmarkdown
Quitting from lines 143-147 (kmedoid.Rmd) 
Error: processing vignette 'kmedoid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kmedoid.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-konfound.Rmd’ using rmarkdown
Quitting from lines 83-84 (introduction-to-konfound.Rmd) 
Error: processing vignette 'introduction-to-konfound.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-konfound.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SAVF_plot
> ### Title: Plot the single attribute value curve
> ### Aliases: SAVF_plot
> 
> ### ** Examples
> 
> 
> # Given the single attribute x is bounded between 1 and 5 and the subject matter experts
> # prefer x values of 3, 4, & 5 provide a utility score of .75, .90 & 1.0 respectively,
> # the preferred rho is 0.54. We can visualize this value function:
> 
> SAVF_plot(desired_x = c(3, 4, 5),
+           desired_v = c(.75, .9, 1),
+           x_low = 1,
+           x_high = 5,
+           rho = 0.54)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘kraljic.Rmd’ using rmarkdown
Quitting from lines 145-152 (kraljic.Rmd) 
Error: processing vignette 'kraljic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kraljic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘L0Learn-vignette.Rmd’ using rmarkdown
Quitting from lines 129-130 (L0Learn-vignette.Rmd) 
Error: processing vignette 'L0Learn-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘L0Learn-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘L0Learn-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘l1kdeconv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmmplot
> ### Title: Plot the Fit Results of 2-Component Gaussian Mixture Model
> ### Aliases: gmmplot
> ### Keywords: distribution
> 
> ### ** Examples
> 
> set.seed(0)
> x=list(c(
+   rnorm(150, mean=0)
+   , rnorm(50, mean=10)
+   ))
> fit_res=multigmmsamedistribu(x)
number of iterations= 7 
> 
> with(
+   as.list(fit_res$par_conv)
+   , gmmplot(x[[1]]
+     , mu1=mu1
+     , mu2=mu2
+     , sigma=sigma
+     , lambda=lambda
+     , xlim=range(unlist(x))
+     )
+   )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘landscapemetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: show_cores
> ### Title: Show core area
> ### Aliases: show_cores show_cores.RasterLayer show_cores.RasterStack
> ###   show_cores.RasterBrick show_cores.stars show_cores.list
> 
> ### ** Examples
> 
> # show "global" core area
> show_cores(landscape, class = "global", labels = FALSE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘landscapetools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: util_merge
> ### Title: util_merge
> ### Aliases: util_merge util_merge.RasterLayer
> 
> ### ** Examples
> 
> x <- util_merge(gradient_landscape, random_landscape)
> show_landscape(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Loading required package: raster
Loading required package: sp
Quitting from lines 31-46 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lans2r-calculate.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 102-109 (lans2r-calculate.Rmd) 
Error: processing vignette 'lans2r-calculate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r-calculate.Rmd’

--- re-building ‘lans2r-hmr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 33-39 (lans2r-hmr.Rmd) 
Error: processing vignette 'lans2r-hmr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r-hmr.Rmd’

--- re-building ‘lans2r.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 92-103 (lans2r.Rmd) 
Error: processing vignette 'lans2r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lans2r.Rmd’

SUMMARY: processing the following files failed:
  ‘lans2r-calculate.Rmd’ ‘lans2r-hmr.Rmd’ ‘lans2r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-latex2exp.Rmd’ using rmarkdown
Quitting from lines 55-71 (using-latex2exp.Rmd) 
Error: processing vignette 'using-latex2exp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-latex2exp.Rmd’

SUMMARY: processing the following file failed:
  ‘using-latex2exp.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lavaSearch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: intDensTri
> ### Title: Integrate a Gaussian/Student Density over a Triangle
> ### Aliases: intDensTri
> 
> ### ** Examples
> 
> library(mvtnorm)
> 
> p <- 2
> Sigma <- diag(p)
> mu <- rep(0, p)
> 
> ## bivariate normal distribution
> z2 <- qmvt(0.975, mean = mu, sigma = Sigma, df = 1e3)$quantile
> 
> # compute integral
> intDensTri(mu = mu, Sigma = Sigma, n=5, x.min=0, type = "fine")$value-1/2
[1] -5.73303e-07
> intDensTri(mu = mu, Sigma = Sigma, n=30, x.min=0, type = "raw")$value-1/2
[1] -0.04696203
> intDensTri(mu = mu, Sigma = Sigma, n=50, x.min=0, type = "raw")$value-1/2
[1] -0.0281983
> 
> intDensTri(mu = mu, Sigma = Sigma, df = 5, n=5, x.min=0, distribution = "pmvt")$value-1/2
[1] -1.814574e-06
> res <- intDensTri(mu = mu, Sigma = Sigma, df = 5, n=10, x.min=0, distribution = "pmvt")
> res$value-1/2
[1] -1.814574e-06
> ggplot2::autoplot(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘LBSPR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSim
> ### Title: General plotting function for simulated data
> ### Aliases: plotSim
> 
> ### ** Examples
> 
>  LB_pars <- new("LB_pars")
A blank LB_pars object created
Default values have been set for some parameters
>  LB_pars@MK <- 1.5
>  LB_pars@Linf <- 100
>  LB_pars@L50 <- 50
>  LB_pars@L95 <- 55
>  LB_pars@SL50 <- 60
>  LB_pars@SL95 <- 65
>  LB_pars@FM <- 1
>  Sim <- LBSPRsim(LB_pars)
BinMax not set. Using default of 1.3 Linf
BinMin not set. Using default value of 0
BinWidth not set. Using default value of 1/20 Linf
>  plotSim(Sim)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotSim ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LBSPR.Rmd’ using rmarkdown
Quitting from lines 233-234 (LBSPR.Rmd) 
Error: processing vignette 'LBSPR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LBSPR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘topics.Rmd’ using rmarkdown
Quitting from lines 84-85 (topics.Rmd) 
Error: processing vignette 'topics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘topics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LDheatmap.Rnw’ using Sweave
Loading required package: grid
--- finished re-building ‘LDheatmap.Rnw’

--- re-building ‘addTracks.Rnw’ using Sweave
Loading required package: survival
Loading required package: Matrix

Error: processing vignette 'addTracks.Rnw' failed with diagnostics:
 chunk 7 (label = fig2) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘addTracks.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LEAP_Vignette.Rnw’ using Sweave
Error: processing vignette 'LEAP_Vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LEAP_Vignette.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_block_summary
> ### Title: Block Summary Plot
> ### Aliases: plot_block_summary
> 
> ### ** Examples
> 
>  
> # A production block runs from unit 201 to unit 500 inclusive.
> # The 201st unit had a required time of 125 hours with a 75% 
> # learning curve. Plot the block summary?
> 
> plot_block_summary(t = 125, m = 201, n = 500, r = .75)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘learningCurve.Rmd’ using rmarkdown
Quitting from lines 170-171 (learningCurve.Rmd) 
Error: processing vignette 'learningCurve.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘learningCurve.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: annotate_y_axis
> ### Title: Annotations in the axis
> ### Aliases: annotate_y_axis annotate_x_axis
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> p <- ggplot(mtcars, aes(mpg, hp, colour=disp)) + geom_point()
> 
> l <- p + annotate_y_axis('mark at', y=200, tick=TRUE)
> l
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘capped-axes.Rmd’ using rmarkdown
Quitting from lines 28-43 (capped-axes.Rmd) 
Error: processing vignette 'capped-axes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘capped-axes.Rmd’

--- re-building ‘facet-rep-labels.Rmd’ using rmarkdown
Quitting from lines 27-29 (facet-rep-labels.Rmd) 
Error: processing vignette 'facet-rep-labels.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘facet-rep-labels.Rmd’

--- re-building ‘geoms.Rmd’ using rmarkdown
Quitting from lines 30-41 (geoms.Rmd) 
Error: processing vignette 'geoms.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geoms.Rmd’

--- re-building ‘gtable_show_lemonade.Rmd’ using rmarkdown
Quitting from lines 22-38 (gtable_show_lemonade.Rmd) 
Error: processing vignette 'gtable_show_lemonade.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gtable_show_lemonade.Rmd’

--- re-building ‘legends.Rmd’ using rmarkdown
Quitting from lines 37-45 (legends.Rmd) 
Error: processing vignette 'legends.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘legends.Rmd’

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

SUMMARY: processing the following files failed:
  ‘capped-axes.Rmd’ ‘facet-rep-labels.Rmd’ ‘geoms.Rmd’
  ‘gtable_show_lemonade.Rmd’ ‘legends.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lexis.cohort
> ### Title: Emphasize a certain cohort in a Lexis grid
> ### Aliases: lexis.cohort
> 
> ### ** Examples
> 
> library(LexisPlotR)
> lg <- lexis.grid(year.start = 1900, year.end = 1905, age.start = 0, age.end = 5)
> lexis.cohort(lg = lg, cohort = 1901)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LexisPlotR.rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 27-29 (LexisPlotR.rmd) 
Error: processing vignette 'LexisPlotR.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LexisPlotR.rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: grid_hexametrics
> ### Title: Area-Based Approach in hexagonal cells.
> ### Aliases: grid_hexametrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
> 
> col = grDevices::colorRampPalette(c("blue", "cyan2", "yellow", "red"))
> 
> # Maximum elevation with a resolution of 8 m
> hm = grid_hexametrics(lidar, max(Z), 8)
> hexbin::plot(hm, colramp = col, main = "Max Z")
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")
Calls: <Anonymous> ... <Anonymous> -> .local -> hexViewport -> <Anonymous>
Execution halted
Running examples in ‘lifelogr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: experiment
> ### Title: Do the specified analysis of the impact of the variables on the
> ###   measure
> ### Aliases: experiment
> 
> ### ** Examples
> 
> data(EX)
> experiment(person = EX, variables = list("fitbit_daily" = c("sleepDuration"),
+                                          "util" = c("day_of_week")),
+                         measures = list("fitbit_daily" = 
+                                           c("restingHeartRate")),
+                         analysis = c("plot"), time_var = c("date"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: experiment ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘summary.Rmd’ using rmarkdown
Quitting from lines 129-130 (summary.Rmd) 
Error: processing vignette 'summary.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘summary.Rmd’

--- re-building ‘vignette_viz.Rmd’ using rmarkdown
Quitting from lines 32-33 (vignette_viz.Rmd) 
Error: processing vignette 'vignette_viz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_viz.Rmd’

SUMMARY: processing the following files failed:
  ‘summary.Rmd’ ‘vignette_viz.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: likert
> ### Title: Analyze Likert type items.
> ### Aliases: likert
> 
> ### ** Examples
> 
> data(pisaitems)
> items29 <- pisaitems[,substr(names(pisaitems), 1,5) == 'ST25Q']
> names(items29) <- c("Magazines", "Comic books", "Fiction", 
+                    "Non-fiction books", "Newspapers")
> l29 <- likert(items29)
> summary(l29)
               Item      low  neutral     high     mean       sd
1         Magazines 30.21689 21.33091 48.45219 3.254813 1.245086
5        Newspapers 37.29377 15.72688 46.97935 3.140282 1.442299
3           Fiction 41.77380 19.61739 38.60882 2.961111 1.342667
2       Comic books 62.43096 15.78368 21.78536 2.298768 1.292631
4 Non-fiction books 61.42466 19.55493 19.02042 2.322898 1.199176
> plot(l29)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> -> print.likert.bar.plot
Execution halted
Running examples in ‘LilRhino-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Monty_Hall
> ### Title: Monty Hall Simulator
> ### Aliases: Monty_Hall
> 
> ### ** Examples
> 
> Monty_Hall(100, 'Stay')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_explanations
> ### Title: Plot a condensed overview of all explanations
> ### Aliases: plot_explanations
> 
> ### ** Examples
> 
> # Create some explanations
> library(MASS)
> iris_test <- iris[1, 1:4]
> iris_train <- iris[-1, 1:4]
> iris_lab <- iris[[5]][-1]
> model <- lda(iris_train, iris_lab)
> explanation <- lime(iris_train, model)
> explanations <- explain(iris_test, explanation, n_labels = 1, n_features = 2)
> 
> # Get an overview with the standard plot
> plot_explanations(explanations)
Error in Summary.unit(c(2, 2), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Quitting from lines 167-168 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Understanding_lime.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_boxcox
> ### Title: Plot boxcox graph in ggplot with suggested lambda transformation
> ### Aliases: gg_boxcox
> 
> ### ** Examples
> 
> library(MASS)
> data(Cars93)
> cars_lm <- lm(Price ~ Passengers + Length + RPM, data = Cars93)
> gg_boxcox(cars_lm)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘linear.tools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deleting_wrongeffect
> ### Title: check monotonicity of marginal impacts and re-estimate the
> ###   model.
> ### Aliases: deleting_wrongeffect
> 
> ### ** Examples
> 
> 
> ##
> set.seed(413)
> traing_data = ggplot2::diamonds[runif(nrow(ggplot2::diamonds))<0.05,]
> nrow(traing_data)
[1] 2642
> 
> diamond_lm3 = lm(formula = price ~ carat + I(carat^2) + I(carat^3) + cut +
+                    I(carat * depth) , data = traing_data)
> 
> 
> test = deleting_wrongeffect(model = diamond_lm3,
+                             focus_var_raw = 'carat',
+                             focus_var_model = c("I(carat^3)","I(carat*depth)",
+                                                 "I(carat^2)","I(carat)"),
+                             focus_value = list(carat=seq(0.5,6,0.1)),
+                             data = traing_data,
+                             PRINT = TRUE,STOP = FALSE,
+                             Reverse = FALSE)

coeff var:  I(carat)  cannot be found in the model, So not check them 

initial model: 
                    Estimate     Pr(>|t|)
(Intercept)        546.06400 2.960453e-03
carat             2592.30091 8.792262e-02
I(carat^2)       10430.65850 3.162007e-76
I(carat^3)       -2614.03182 5.320933e-68
cut.L              753.86085 1.967355e-10
cut.Q             -147.90059 1.474569e-01
cut.C              309.85410 4.583125e-04
cut^4              184.88962 1.151290e-02
I(carat * depth)   -97.58333 1.408239e-05


check raw var:  carat 
check model var:  I(carat^3), I(carat*depth), I(carat^2) 
Correct Monotonicity is supposed to be:  Increasing 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: deleting_wrongeffect ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linear.tools.Rmd’ using rmarkdown
Quitting from lines 157-162 (linear.tools.Rmd) 
Error: processing vignette 'linear.tools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘linear.tools.Rmd’

SUMMARY: processing the following file failed:
  ‘linear.tools.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build.rule
> ### Title: Low-level Functions for Handling List-based Rules
> ### Aliases: build.rule build.rule.cv apply.rule show.rule verbalize.rule
> ###   draw.rule
> ### Keywords: tree
> 
> ### ** Examples
> 
>   x <- matrix(rnorm(200 * 10), 200, 10)
>   y <- cbind(
+     a1 = as.double(x[, 1] < 0) + rnorm(200, 0, 0.1),
+     a2 = as.double(x[, 2] > 0) + rnorm(200, 0, 0.1))
>   y[y < 0] <- 0
>   
>   obj <- build.rule(x, y)
>   show.rule(obj)
If x2 <= -0.064 then a2;
If x1 > 0.015 then a1;
If x10 <= -2.209 then a2;
If x1 > -0.009 then a1;
If x2 <= -0.002 then a2;
If x2 > 2.573 then a2;
If x9 > 2.388 then a1;
If x9 > 1.616 then a1;
If x7 > 2.499 then a1;
Else a2.
>   draw.rule(obj)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wine_quality.Rmd’ using rmarkdown
Loading required package: ParamHelpers
Welcome to live v1.5.10. Live is a part of DALEXverse. Find out more at https://github.com/pbiecek/DALEX.

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: 'e1071'

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

    impute

Warning: Ignoring unknown aesthetics: x
Quitting from lines 98-99 (wine_quality.Rmd) 
Error: processing vignette 'wine_quality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wine_quality.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AQSys.plot
> ### Title: Dataset and Fitted Function plot
> ### Aliases: AQSys.plot
> 
> ### ** Examples
> 
> #Populating variable dataSET with binodal data
> dataSET <- peg4kslt[, 1:2]
> # Plot dataSET using Merchuk's function
> #
> AQSys.plot(dataSET)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: AQSys.plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘lme4-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: profile-methods
> ### Title: Profile method for merMod objects
> ### Aliases: as.data.frame.thpr log.thpr logProf varianceProf
> ###   profile-methods profile.merMod
> ### Keywords: methods
> 
> ### ** Examples
> 
> fm01ML <- lmer(Yield ~ 1|Batch, Dyestuff, REML = FALSE)
> system.time(
+   tpr  <- profile(fm01ML, optimizer="Nelder_Mead", which="beta_")
+ )## fast; as only *one* beta parameter is profiled over
   user  system elapsed 
  0.282   0.008   0.290 
> ## full profiling (default which means 'all) needs
> ## ~2.6s (on a 2010 Macbook Pro)
> system.time( tpr  <- profile(fm01ML))
   user  system elapsed 
  0.706   0.004   0.712 
> ## ~1s, + possible warning about bobyqa convergence
> (confint(tpr) -> CIpr)
                 2.5 %     97.5 %
.sig01        12.19853   84.06305
.sigma        38.22998   67.65770
(Intercept) 1486.45150 1568.54849
> library("lattice")
> xyplot(tpr)
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: <Anonymous> ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lmerperf.Rmd’ using rmarkdown
--- finished re-building ‘lmerperf.Rmd’

--- re-building ‘lmer.Rnw’ using knitr
Loading required package: Matrix
Computing profile confidence intervals ...
Computing bootstrap confidence intervals ...

7 message(s): boundary (singular) fit: see ?isSingular
186 warning(s): Model failed to converge with max|grad| = 0.00203996 (tol = 0.002, component 1) (and others)

Quitting from lines 2656-2657 (lmer.Rnw) 
Error: processing vignette 'lmer.Rnw' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘lmer.Rnw’

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

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LocalControl-jss-2018.Rnw’ using Sweave
Loading required package: data.table
Loading required package: colorspace
Loading required package: RColorBrewer
Loading required package: gridExtra
Loading required package: ggplot2
Loading required package: rpart
Loading required package: rpart.plot
Loading required package: LocalControl
Loading required package: xtable
Loading required package: TeachingDemos

Attaching package: 'TeachingDemos'

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

    digits


Error: processing vignette 'LocalControl-jss-2018.Rnw' failed with diagnostics:
 chunk 31 (label = figure_8) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building 'LocalControl-jss-2018.Rnw'

SUMMARY: processing the following file failed:
  'LocalControl-jss-2018.Rnw'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localfdr-intro-vignette.Rmd’ using rmarkdown
Quitting from lines 137-138 (localfdr-intro-vignette.Rmd) 
Error: processing vignette 'localfdr-intro-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘localfdr-intro-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logihist
> ### Title: Combined Graphs for Logistic Regression
> ### Aliases: logihist logibox logidot
> ### Keywords: ~aplot
> 
> ### ** Examples
> 
> 
> # Get some data from package popbio
> data(aq.trans, package="popbio")
> aq.trans$survived<-aq.trans$fate!="dead"
> a<-subset(aq.trans, leaf<50 & stage!="recruit", c(leaf,survived))
> 
> 
> # Transform the "survived" variable in numeric
> # This is necesary to correctly plot the combined graph.
>  
> a$survived <-a$survived*1
> 
> # Fit a logistic regression
> glm.a<- glm(survived~leaf, data=a, family=binomial)
> 
> 
> # Histograms
> # From individual variables
> # Modifying the appearence of histogram bins
> logihist(a$leaf,a$survived)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘logisticPCA.Rmd’ using rmarkdown
Quitting from lines 112-114 (logisticPCA.Rmd) 
Error: processing vignette 'logisticPCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘logisticPCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘logitnorm.Rmd’ using knitr
Quitting from lines 45-76 (logitnorm.Rmd) 
Error: processing vignette 'logitnorm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘logitnorm.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘aggregateCorrelated.Rmd’ using rmarkdown
Quitting from lines 70-77 (aggregateCorrelated.Rmd) 
Error: processing vignette 'aggregateCorrelated.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘aggregateCorrelated.Rmd’

--- re-building ‘lognorm.Rmd’ using rmarkdown
Quitting from lines 51-78 (lognorm.Rmd) 
Error: processing vignette 'lognorm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lognorm.Rmd’

--- re-building ‘lognormalSum.Rmd’ using rmarkdown
Quitting from lines 56-75 (lognormalSum.Rmd) 
Error: processing vignette 'lognormalSum.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lognormalSum.Rmd’

SUMMARY: processing the following files failed:
  ‘aggregateCorrelated.Rmd’ ‘lognorm.Rmd’ ‘lognormalSum.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp: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-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘lolog-ergm.Rmd’ using rmarkdown
Quitting from lines 69-75 (lolog-ergm.Rmd) 
Error: processing vignette 'lolog-ergm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lolog-ergm.Rmd’

--- re-building ‘lolog-introduction.Rmd’ using rmarkdown
Quitting from lines 406-409 (lolog-introduction.Rmd) 
Error: processing vignette 'lolog-introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lolog-introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  ── 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  ─────────────────
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘longitudinalcascade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: longitudinalcascade
> ### Title: Longitudinal cascade statistics and charts
> ### Aliases: longitudinalcascade
> ### Keywords: cascade longitudinal survival
> 
> ### ** Examples
> 
> # Pull in data from example simulated dataset
> library(longitudinalcascade)
> data(events_long)
> 
> # Set up options
> stages.order <- c("First tested positive","Knows status","Linked to care","Eligible for ART",
+ "Initiated ART","Therapeutic response")
> groups.order <- c("Group 1","Group 2","Group 3")
> death.indicator <- "Death"
> retention.indicator <- "Clinic visit"
> censorship.indicator <- "LTFU"
> allow.sub.lines <- TRUE
> allow.skips <- TRUE
> 
> # Create cascade object
> longitudinalcascade.sim <- longitudinalcascade(events_long,stages.order=stages.order,
+ groups.order=groups.order,death.indicator=death.indicator,
+ censorship.indicator=censorship.indicator,
+ allow.sub.lines=allow.sub.lines,allow.skips=allow.skips)
> 
> # Print/output main chart
> longitudinalcascade.sim$chart
Error in Summary.unit(c(0, 0), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘loose.rock-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw.cov.matrix
> ### Title: Plot covariance heatmap from matrix
> ### Aliases: draw.cov.matrix
> 
> ### ** Examples
> 
> draw.cov.matrix(matrix(rnorm(100), ncol = 10))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [10s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loose.rock)
  > 
  > test_check("loose.rock")
  ── 1. Error: single multiplot (@test-multiplot.R#4)  ───────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(multiplot(ggplot2::qplot(1:10, 11:20))) at testthat/test-multiplot.R:4
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: multiplot(ggplot2::qplot(1:10, 11:20))
  10: print(plots[[1]])
  ...
  16: preDraw(x)
  17: preDraw.gTree(x)
  18: pushvpgp(x)
  19: pushgrobvp(x$vp)
  20: pushgrobvp.viewport(x$vp)
  21: pushViewport(vp, recording = FALSE)
  22: lapply(vps, push.vp, recording)
  23: FUN(X[[i]], ...)
  24: push.vp.viewport(X[[i]], ...)
  25: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 144 SKIPPED: 0 FAILED: 1
  1. Error: single multiplot (@test-multiplot.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Prefixing `UQ()` with the rlang namespace is deprecated as of rlang 0.3.0.
Please use the non-prefixed form or `!!` instead.

  # Bad:
  rlang::expr(mean(rlang::UQ(var) * 100))

  # Ok:
  rlang::expr(mean(UQ(var) * 100))

  # Good:
  rlang::expr(mean(!!var * 100))

This warning is displayed once per session.
Quitting from lines 112-126 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lpdensity.plot
> ### Title: Local Polynomial Density Plot with Robust Confidence Intervals
> ### Aliases: lpdensity.plot
> 
> ### ** Examples
> 
> set.seed(42); X <- rnorm(2000)
> 
> X <- X - 0.5; X[X>0] <- X[X>0] * 2
> est1 <- lpdensity(data = X[X<=0], grid = seq(-2.5, 0, 0.05), bwselect = "IMSE",
+   scale = sum(X<=0)/length(X))
> est2 <- lpdensity(data = X[X>0],  grid = seq(0, 2, 0.05), bwselect = "IMSE",
+   scale = sum(X>0)/length(X))
> lpdensity.plot(est1, est2, legendTitle="My Plot", legendGroups=c("Left", "Right"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LPWC.Rmd’ using rmarkdown
Quitting from lines 145-173 (LPWC.Rmd) 
Error: processing vignette 'LPWC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘LPWC.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meanbiplot
> ### Title: Biplots of
> ### Aliases: meanbiplot
> 
> ### ** Examples
> 
> set.seed(1)
> dat <- rlsbclust(ndata = 1, nobs = 100, size = c(10, 8), nclust = c(5, 4, 6, 5))
> meanbiplot(dat[[1]]$interactions$C, dat[[1]]$interactions$D)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  ── 1. Failure: cluster vector (@test_orc.R#29)  ────────────────────────────────
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  ── 2. Failure: cluster means (@test_orc.R#33)  ─────────────────────────────────
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘lsl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lslSEM-class
> ### Title: A Reference Class for Learning a SEM model via penalized
> ###   likelihood.
> ### Aliases: lslSEM-class lslSEM
> 
> ### ** Examples
> 
> #Example: Holzinger and Swineford (1939) Data#
> lambda <- matrix(NA, 9, 3)
> lambda[c(1,2,3), 1] <- lambda[c(4,5,6), 2] <- lambda[c(7,8,9), 3] <- 1
> 
> rc_sem <- lslSEM()
> rc_sem$input(raw = lavaan::HolzingerSwineford1939)
> rc_sem$specify(pattern = list(lambda = lambda))
> rc_sem$learn(penalty = list(type = "l1", gamma = seq(.05, .10, .05)), variable = 7:15)
> rc_sem$draw(type = "individual", object = "lambda")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘factor-analysis.Rmd’ using rmarkdown
Quitting from lines 100-101 (factor-analysis.Rmd) 
Error: processing vignette 'factor-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘factor-analysis.Rmd’

--- re-building ‘missing-data-analysis.Rmd’ using rmarkdown
--- finished re-building ‘missing-data-analysis.Rmd’

--- re-building ‘multi-group-analysis.Rmd’ using rmarkdown
--- finished re-building ‘multi-group-analysis.Rmd’

--- re-building ‘regression-analysis.Rmd’ using rmarkdown
Quitting from lines 89-90 (regression-analysis.Rmd) 
Error: processing vignette 'regression-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘regression-analysis.Rmd’

--- re-building ‘structural-equation-modeling.Rmd’ using rmarkdown
--- finished re-building ‘structural-equation-modeling.Rmd’

SUMMARY: processing the following files failed:
  ‘factor-analysis.Rmd’ ‘regression-analysis.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lsprobust.plot
> ### Title: Graphic Presentation of Results for 'lspartition' Package
> ### Aliases: lsprobust.plot
> 
> ### ** Examples
> 
> x   <- runif(500)
> y   <- sin(4*x)+rnorm(500)
> est <- lsprobust(y, x)
> lsprobust.plot(est)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Quitting from lines 69-75 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘lspline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom-models.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
--- finished re-building ‘custom-models.Rmd’

--- re-building ‘example-plots.Rmd’ using knitr
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 24-59 (example-plots.Rmd) 
Error: processing vignette 'example-plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘example-plots.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LTRCART
> ### Title: Fit a relative risk survival tree for LTRC data
> ### Aliases: LTRCART
> 
> ### ** Examples
> 
> ## The Assay of serum free light chain data in survival package
> ## Adjust data & clean data
> library(survival)
> library(LTRCtrees)
> Data <- flchain
> Data <- Data[!is.na(Data$creatinine),]
> Data$End <- Data$age + Data$futime/365
> DATA <- Data[Data$End > Data$age,]
> names(DATA)[6] <- "FLC"
> 
> ## Setup training set and test set
> Train = DATA[1:500,]
> Test = DATA[1000:1020,]
> 
> ## Fit LTRCART survival tree
> ## make sure to attach survival package (by library(survival) ) before using Surv function
> LTRCART.obj <- LTRCART(Surv(age, End, death) ~ sex + FLC + creatinine, Train)
> 
> ## Putting Surv(End, death) in formula would result an error message
> ## since LTRCART is expecting Surv(time1, time2, event)
> 
> ## Plot the fitted tree
> library(rpart.plot)
Loading required package: rpart

Attaching package: ‘rpart’

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

    solder

> rpart.plot(LTRCART.obj)
Warning: Cannot retrieve the data used to build the model (model.frame: object 'Newtime' not found).
To silence this warning:
    Call rpart.plot with roundint=FALSE,
    or rebuild the rpart model with model=TRUE.
> 
> ## Plot as partykit::party object
> library(partykit)
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
> plot(as.party(LTRCART.obj))
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
Quitting from lines 48-62 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘LTRCtrees.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_lv
> ### Title: Side-by-side LV boxplots with ggplot2.
> ### Aliases: GeomLv StatLv geom_lv scale_fill_lv stat_lv
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(mpg, aes(class, hwy))
> p + geom_lv(aes(fill=..LV..)) + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using rmarkdown
Quitting from lines 266-272 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calibration
> ### Title: Model Calibration
> ### Aliases: calibration Calibration
> 
> ### ** Examples
> 
> library(survival)
> library(MASS)
> 
> res <- resample(Surv(time, status != 2) ~ sex + age + year + thickness + ulcer,
+                 data = Melanoma, model = GBMModel,
+                 control = CVControl(times = 365 * c(2, 5, 10)))
> cal <- calibration(res)
> plot(cal)
$GBMModel
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning: Removed 70 rows containing missing values (geom_point).
Quitting from lines 126-136 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘macleish.Rmd’ using rmarkdown
Loading required package: etl
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date

Loading required package: mgcv
Loading required package: nlme

Attaching package: 'nlme'

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

    collapse

This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Quitting from lines 94-104 (macleish.Rmd) 
Error: processing vignette 'macleish.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘macleish.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘maddison_project_database.Rmd’ using rmarkdown
Warning: Removed 20 rows containing missing values (geom_path).
Quitting from lines 41-51 (maddison_project_database.Rmd) 
Error: processing vignette 'maddison_project_database.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘maddison_project_database.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotcon
> ### Title: Meta Regression Scatterplot
> ### Aliases: plotcon
> ### Keywords: aplot
> 
> ### ** Examples
> 
> # SAMPLE DATA
> MA2 <-read.table(textConnection("
+ id       es1       var1 n.1 n.2 mod1 mod2
+ 1   1 0.5695938 0.04906967  26  30    a   20
+ 2   2 0.4123667 0.04362541  28  34    b   30
+ 3   3 0.4084333 0.04458363  34  28    a   25
+ 4   4 0.5014756 0.04186354  37  29    b   35
+ 5   5 0.5540745 0.04339382  31  32    b   40
+ 6   1 0.5695938 0.04906967  26  30    a   20
+ 7   2 0.4123667 0.04362541  28  34    b   30
+ 8   3 0.4084333 0.04458363  34  28    a   25
+ 9   4 0.5014756 0.04186354  37  29    b   35
+ 10  5 0.5540745 0.04339382  31  32    b   40"))
> 
> 
> # EXAMPLE
> plotcon(es1, var1, mod2, data=MA2, method= "fixed", modname="NULL",title="NULL")
Loading required package: ggplot2
Loading required package: metafor
Loading required package: Matrix
Loading 'metafor' package (version 2.0-0). For an overview 
and introduction to the package please type: help(metafor).
Warning in model.matrix.default(terms, mf, contrasts) :
  non-list contrasts argument ignored
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mafs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_fit
> ### Title: Graphical results of forecast models
> ### Aliases: gg_fit
> 
> ### ** Examples
> 
> gg_fit(AirPassengers, 12, "snaive")
Warning: Removed 156 rows containing missing values (geom_path).
Warning: Removed 12 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 414-418 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
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 105-106 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘manhattanly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Running examples in ‘mapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hull
> ### Title: Add a convex hull to a map
> ### Aliases: hull
> 
> ### ** Examples
> 
> # map spocc output, here using a built in object
> data(occdat_eg1)
> map_plot(occdat_eg1, hull = TRUE)
> 
> # map rgbif output, here using a built in object
> hull(map_ggplot(occdat_eg1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘markedVignette.Rnw’ using Sweave
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.2.1

Model: CJS

Processing data...

255 capture histories collapsed into 53
Creating design data...

Fitting model

Computing initial parameter estimates

Starting optimization for 2 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 4 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 8 parameters...
255 capture histories collapsed into 53
Fitting model

Computing initial parameter estimates

Starting optimization for 3 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 4 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Fitting model

Computing initial parameter estimates

Starting optimization for 8 parameters...
255 capture histories collapsed into 171
Fitting model

Computing initial parameter estimates

Starting optimization for 7 parameters...
Computing hessian...
Error: processing vignette 'markedVignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘markedVignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MarketMatching-Vignette.Rmd’ using rmarkdown_notangle
Quitting from lines 109-110 (MarketMatching-Vignette.Rmd) 
Error: processing vignette 'MarketMatching-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MarketMatching-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MarketMatching-Vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: etopo
> ### Title: Etopo colours
> ### Aliases: etopo etopo.colors etopo.colours scale_color_etopo
> ###   scale_colour_etopo scale_fill_etopo
> 
> ### ** Examples
> 
> # load NW Atlantic data and convert to class bathy
> data(nw.atlantic)
> atl <- as.bathy(nw.atlantic)
> 
> # plot with base graphics
> plot(atl, image=TRUE)
> 
> # using the etopo color scale
> etopo_cols <- rev(etopo.colors(8))
> plot(atl, image=TRUE, bpal=list(
+   c(min(atl), 0, etopo_cols[1:2]),
+   c(0, max(atl), etopo_cols[3:8])
+ ))
> 
> 
> # plot using ggplot2; in which case the limits of the scale are automatic
> library("ggplot2")
> ggplot(atl, aes(x=x, y=y)) + coord_quickmap() +
+   # background
+   geom_raster(aes(fill=z)) +
+   scale_fill_etopo() +
+   # countours
+   geom_contour(aes(z=z),
+     breaks=c(0, -100, -200, -500, -1000, -2000, -4000),
+     colour="black", size=0.2
+   ) +
+   scale_x_continuous(expand=c(0,0)) +
+   scale_y_continuous(expand=c(0,0))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
> library(ggplot2)
> theme_set(theme_bw())
> 
> # Make a plot of the observations and model fits
> d <- augment(MLEobj, interval="confidence")
> ggplot(data = d) + 
+   geom_line(aes(t, .fitted)) +
+   geom_point(aes(t, y)) +
+   geom_ribbon(aes(x=t, ymin=.conf.low, ymax=.conf.up), linetype=2, alpha=0.1) +
+   facet_grid(~.rownames) +
+   xlab("Time Step") + ylab("Count")
Warning: Removed 24 rows containing missing values (geom_point).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘matching.Rnw’ using knitr_notangle
Quitting from lines 65-75 (././Sections/4_MonteCarloResults.Rnw) 
Quitting from lines 39-40 (././Sections/4_MonteCarloResults.Rnw) 
Error: processing vignette 'matching.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘matching.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘matsindf.Rmd’ using rmarkdown
Quitting from lines 385-397 (matsindf.Rmd) 
Error: processing vignette 'matsindf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘matsindf.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Sim.Const.Weights
> ### Title: Simulation of constrained weights
> ### Aliases: Sim.Const.Weights
> 
> ### ** Examples
> 
> library( data.table )
> N<-10
> utilities<-data.table( id = 1:N, 
+                        u1 = runif( N, 0, 1 ), 
+                        u2 = runif( N, 0, 1 ), 
+                        u3 = runif( N, 0, 1 ),
+                        u4 = runif( N, 0, 1 ) )
> n<-100
> alpha<-c( 0.2, 0.5, 0.1, 0.2 )
> constraints<-list( list( c(1,2), 0.7 ), 
+                    list( c(3,4), 0.3 ) )
> S<-Sim.Const.Weights( n, utilities, alpha, constraints )
> plot.S<-Plot.Simulation.Weight( S$simulation, title = 'Simulations', 
+                                 xlab = 'ID', ylab = 'Utility' ) 
> plot( plot.S )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running_MAUT.Rmd’ using rmarkdown

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 150-158 (Running_MAUT.Rmd) 
Error: processing vignette 'Running_MAUT.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Running_MAUT.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.MCAvariants
> ### Title: Main plot function for classical and ordered multiple
> ###   correspondence analysis
> ### Aliases: plot.MCAvariants
> ### Keywords: graphical
> 
> ### ** Examples
> 
> data(satisfaction)
> ris1=MCAvariants(satisfaction, catype = "mca")
> plot.MCAvariants(ris1)
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot.MCAvariants ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mccf1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mccf1
> ### Title: Plot the MCC-F1 curve
> ### Aliases: plot.mccf1
> 
> ### ** Examples
> 
> response <- c(rep(1, 1000), rep(0, 10000))
> predictor <- c(rbeta(300, 12, 2), rbeta(700, 3, 4), rbeta(10000, 2, 3))
> plot(mccf1(response, predictor))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mcmcabn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mcmcabn
> ### Title: Function to plot mcmcabn class objects
> ### Aliases: plot.mcmcabn
> 
> ### ** Examples
> 
> ## Example from the asia dataset from Lauritzen and Spiegelhalter (1988) provided by Scutari (2010)
> data("mcmc_run_asia")
> 
> #plot the mcmc run
> plot(mcmc.out.asia)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcmcabn.Rmd’ using rmarkdown

Attaching package: 'bnlearn'

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

    sigma

Loading required package: nnet
Loading required package: Cairo
Loading required package: MASS
Loading required package: lme4
Loading required package: Matrix

Attaching package: 'abn'

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

    mb

Loading required package: magrittr

Attaching package: 'magrittr'

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

    or


Attaching package: 'cowplot'

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

    get_legend

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

    ggsave


Attaching package: 'ggdag'

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

    expand_scale

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

    filter

Quitting from lines 79-111 (mcmcabn.Rmd) 
Error: processing vignette 'mcmcabn.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mcmcabn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Generation.Rmd’ using rmarkdown
Loading required package: BBmisc

Attaching package: 'BBmisc'

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

    isFALSE

Loading required package: ecr
Loading required package: smoof
Loading required package: ParamHelpers
Loading required package: checkmate
Quitting from lines 30-36 (Generation.Rmd) 
Error: processing vignette 'Generation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Generation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: BBmisc

Attaching package: 'BBmisc'

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

    isFALSE

Loading required package: ecr
Loading required package: smoof
Loading required package: ParamHelpers
Loading required package: checkmate
Quitting from lines 28-39 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Mdata
> ### Title: Plotting M Competition data
> ### Aliases: plot.Mdata autoplot.Mdata autoplot.Mdata
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> plot(M1[[1]])
> autoplot(M1$YAF3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mcprofile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hoa
> ### Title: Higher order asymptotics using the modified likelihood root
> ### Aliases: hoa
> ### Keywords: misc
> 
> ### ** Examples
> 
> #######################################
> ## cell transformation assay example ##
> #######################################
> 
> str(cta)
'data.frame':	80 obs. of  2 variables:
 $ conc: num  0 0 0 0 0 0 0 0 0 0 ...
 $ foci: int  0 1 0 0 0 0 0 0 0 2 ...
> ## change class of cta$conc into factor
> cta$concf <- factor(cta$conc, levels=unique(cta$conc))
> 
> ggplot(cta, aes(y=foci, x=concf)) + 
+    geom_boxplot() +
+    geom_dotplot(binaxis = "y", stackdir = "center", binwidth = 0.2) +    
+    xlab("concentration")
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mcprofile.Rmd’ using knitr
Loading required package: ggplot2
Quitting from lines 111-119 (mcprofile.Rmd) 
Error: processing vignette 'mcprofile.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mcprofile.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Adj2Lap
> ### Title: Compute graph Laplacian matrix from graph adjacency matrix
> ### Aliases: Adj2Lap
> 
> ### ** Examples
> 
> # Define exemplary adjacency matrix
> p1 <- 10
> p2 <- 40
> p <- p1 + p2
> A <- matrix(rep(0, p * p), p, p)
> A[1:p1, 1:p1] <- 1
> A[(p1 + 1):p, (p1 + 1):p] <- 1
> vizu.mat(A, "adjacency matrix")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_and_usage_examples.Rmd’ using rmarkdown
Quitting from lines 62-79 (Intro_and_usage_examples.Rmd) 
Error: processing vignette 'Intro_and_usage_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_and_usage_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_input.Rmd’ using rmarkdown
--- finished re-building ‘data_input.Rmd’

--- re-building ‘meaRtoolsGeneralUsage.Rmd’ using rmarkdown
Quitting from lines 374-380 (meaRtoolsGeneralUsage.Rmd) 
Error: processing vignette 'meaRtoolsGeneralUsage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘meaRtoolsGeneralUsage.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette 'advanced.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘advanced.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cost-report-analysis.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Joining, by = "rpt_rec_num"
Quitting from lines 164-189 (cost-report-analysis.Rmd) 
Error: processing vignette 'cost-report-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cost-report-analysis.Rmd’

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

SUMMARY: processing the following file failed:
  ‘cost-report-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MEGENA_pipeline_10062016.Rmd’ using rmarkdown
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 120-128 (MEGENA_pipeline_10062016.Rmd) 
Error: processing vignette 'MEGENA_pipeline_10062016.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MEGENA_pipeline_10062016.Rmd’

SUMMARY: processing the following file failed:
  ‘MEGENA_pipeline_10062016.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: barmekko
> ### Title: Create a bar mekko plot.
> ### Aliases: barmekko
> 
> ### ** Examples
> 
> library(ggplot2)
> df <- data.frame(
+   region = c('Northeast', 'Southeast', 'Central', 'West'),
+   sales = c(1200, 800, 450, 900),
+   avg_margin = c(3.2, -1.4, 0.1, 2.1)
+   )
> barmekko(df, region, avg_margin, sales)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mekko-vignette.Rmd’ using rmarkdown
Quitting from lines 58-60 (mekko-vignette.Rmd) 
Error: processing vignette 'mekko-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mekko-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘meme.Rmd’ using rmarkdown
Quitting from lines 167-177 (meme.Rmd) 
Error: processing vignette 'meme.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘meme.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meme
> ### Title: Generate a meme
> ### Aliases: meme meme meme_gif
> 
> ### ** Examples
> 
> # Prepare data and make a graph
> library(ggplot2)
> x <- seq(0, 2*pi, length.out = 50)
> panels <- rep(c("Plot A", "Plot B"), each = 50)
> d <- data.frame(x = x, y = sin(x), grp = panels)
> txt <- c("Philosoraptor's plots", "I like to make plots",
+   "Figure 1. (A) shows a plot and (B) shows another plot.")
> 
> p <- ggplot(d, aes(x, y)) + geom_line(colour = "cornflowerblue", size = 2) +
+   geom_point(colour = "orange", size = 4) + facet_wrap(~grp) +
+   labs(title = txt[1], subtitle = txt[2], caption = txt[3])
> 
> # meme image background and text labels
> img <- system.file("philosoraptor.jpg", package = "memery")
> lab <- c("Title meme text", "Subtitle text")
> 
> ## Not run: 
> ##D 
> ##D # Not run due to file size
> ##D # basic meme
> ##D meme(img, lab[1:2], "meme_basic.jpg")
> ##D # data analyst's meme
> ##D meme(img, lab[1:2], "meme_data.jpg", size = 2, inset = p, mult = 2)
> ## End(Not run)
> 
> # data meme with additional content control
> vp_bg <- list(fill = "#FF00FF50", col = "#FFFFFF80") # graph background
> # arbitrary number of labels, placement, and other vectorized attributes
> lab <- c(lab, "Middle plot text")
> pos <- list(w = rep(0.9, 3), h = rep(0.3, 3), x = c(0.35, 0.65, 0.5),
+   y = c(0.95, 0.85, 0.3))
> fam <- c("Impact", "serif", "Impact")
> clrs1 <- c("black", "orange", "white")
> clrs2 <- clrs1[c(2, 1, 1)]
> meme(img, lab, "meme_data2.jpg", size = c(2, 1.5, 1), family = fam, col = clrs1,
+   shadow = clrs2, label_pos = pos, inset = p, inset_bg = vp_bg, mult = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: meme ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(memery)
  Loading required package: showtext
  Loading required package: sysfonts
  Loading required package: showtextdb
  > 
  > test_check("memery")
  ── 1. Error: meme runs as expected (@test-meme.R#24)  ──────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(meme(loc, lab[1], out[1]), x) at testthat/test-meme.R:24
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: meme(loc, lab[1], out[1])
  5: print(p0, vp = vp_back)
  6: print.ggplot(p0, vp = vp_back)
  7: grid.draw(gtable)
  8: grid.draw.gTree(gtable)
  9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  10: drawGTree(x)
  11: preDraw(x)
  12: preDraw.gTree(x)
  13: pushvpgp(x)
  14: pushgrobvp(x$vp)
  15: pushgrobvp.viewport(x$vp)
  16: pushViewport(vp, recording = FALSE)
  17: lapply(vps, push.vp, recording)
  18: FUN(X[[i]], ...)
  19: push.vp.viewport(X[[i]], ...)
  20: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 3 FAILED: 1
  1. Error: meme runs as expected (@test-meme.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘memery.Rmd’ using rmarkdown
Loading required package: showtext
Loading required package: sysfonts
Loading required package: showtextdb
Quitting from lines 19-23 (memery.Rmd) 
Error: processing vignette 'memery.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘memery.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mr_plot
> ### Title: Draw a scatter plot of the genetic associations and/or causal
> ###   estimates
> ### Aliases: mr_plot mr_plot,MRInput-method mr_plot,MRAll-method
> 
> ### ** Examples
> 
> mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
+   line="egger", orientate = TRUE)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: mr_plot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette_MR.Rmd’ using rmarkdown
Quitting from lines 338-340 (Vignette_MR.Rmd) 
Error: processing vignette 'Vignette_MR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vignette_MR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotFEsim
> ### Title: Plot the results of a simulation of the fixed effects
> ### Aliases: plotFEsim
> 
> ### ** Examples
> 
>  fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
>  (p1 <- plotFEsim(FEsim(fm1)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘MetaComp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_edge_assignment
> ### Title: Generates a single column ggplot for a taxonomic assignment
> ###   table and also outputs a PDF.
> ### Aliases: plot_edge_assignment
> 
> ### ** Examples
> 
> pa_fpath <- system.file("extdata", "HMP_even//allReads-pangia.list.txt", package="MetaComp")
> pangia_assignment = load_edge_assignment(pa_fpath, type = "pangia")
> 
> plot_edge_assignment(pangia_assignment, "phylum", "Pangia", "HMP Even",
+                                                      file.path(tempdir(), "assignment.pdf"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_edge_assignment ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metaforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClusterMF
> ### Title: Clustered MetaForest analysis for dependent data.
> ### Aliases: ClusterMF
> 
> ### ** Examples
> 
> #Load and clean data from metafor
> data <- get(data(dat.bourassa1996))
> data <- escalc(measure = "OR", ai = lh.le, bi = lh.re, ci = rh.le, di= rh.re,
+                data = data, add = 1/2, to = "all")
> data$mage[is.na(data$mage)] <- median(data$mage, na.rm = TRUE)
> data[c(5:8)] <- lapply(data[c(5:8)], factor)
> data$yi <- as.numeric(data$yi)
> mf.cluster.b1996 <- ClusterMF(formula = yi~ selection + investigator +
+                               hand_assess + eye_assess + mage +sex,
+                               data, study = "sample",
+                               whichweights = "unif", num.trees = 300)
> #Print MetaForest object
> mf.cluster.b1996
Call:
ClusterMF(formula = yi ~ selection + investigator + hand_assess + 
    eye_assess + mage + sex, data = data, study = "sample", whichweights = "unif", 
    num.trees = 300)

R squared (OOB):                  0.0231 
Residual heterogeneity (tau2):    0.3075 
> #Check convergence plot
> plot(mf.cluster.b1996)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metagen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensityH
> ### Title: Pivotal distributions: Plot pivotal distribution of
> ###   heterogeneity
> ### Aliases: plotDensityH
> 
> ### ** Examples
> 
> bcg   <- bcgVaccineData()
> bcg_y <- bcg$logrisk
> bcg_d <- bcg$sdiv
> bcg_s <- bcg$size
> bcg_x <- cbind(1,bcg$x)
> 
> set.seed(865287113)
> pivUn <- pivotalStream(50, y=bcg_y, d=bcg_d, x=bcg_x,
+   adjusted=FALSE)
> set.seed(865287113)
> pivAd <- pivotalStream(50, y=bcg_y, d=bcg_d, x=bcg_x, s=bcg_s,
+   adjusted=TRUE)
> 
> pivh <- joinPivotalHeterogeneity(pivUn, pivAd)
> plotDensityH(pivh)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metaheur-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotsearchpath
> ### Title: plot search path
> ### Aliases: plotsearchpath
> 
> ### ** Examples
> 
> plotsearchpath(examplesearch)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Metaheur.Rmd’ using rmarkdown
Quitting from lines 79-80 (Metaheur.Rmd) 
Error: processing vignette 'Metaheur.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Metaheur.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggForestPlot
> ### Title: Compare effect sizes of a gene across all datasets in
> ###   meta-analysis
> ### Aliases: ggForestPlot
> ### Keywords: graphs hplot
> 
> ### ** Examples
> 
> # compare effect sizes of the Gene1 for all discovery datasets in tinyMetaObject 
> ggForestPlot(tinyMetaObject, genes="Gene1")
Warning: Removed 2 rows containing missing values (geom_errorbarh).
Warning: Removed 2 rows containing missing values (geom_point).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
Quitting from lines 187-188 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaIntegrator.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visualizeFeature
> ### Title: Visualize Longitudinal Feature
> ### Aliases: visualizeFeature
> 
> ### ** Examples
> 
> data(metalonda_test_data)
> n.sample = 5
> n.timepoints = 10
> n.group = 2
> Group = factor(c(rep(0, n.sample*n.timepoints), rep(1, n.sample*n.timepoints)))
> Time = rep(rep(1:n.timepoints, times = n.sample), 2)
> ID = factor(rep(1:(2*n.sample), each = n.timepoints))
> points = seq(1, 10, length.out = 10)
> aggregate.df = data.frame(Count = metalonda_test_data[1,], Time = Time, Group = Group, ID = ID)
> visualizeFeature(aggregate.df, text = rownames(metalonda_test_data)[1], Group)
Visualizing Feature =  OTU_1 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: visualizeFeature ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaLonDA.Rmd’ using knitr
Quitting from lines 68-73 (MetaLonDA.Rmd) 
Error: processing vignette 'MetaLonDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaLonDA.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Zhang
> ### Title: Meta-analysis of the prognostic role of hormone receptors in
> ###   endometrial cancer
> ### Aliases: Zhang
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Zhang)
> 
> # Display the hazard ratios for overall survival in a forest plot
> ds <- subset(Zhang, outcome=="OS")
> with(ds, forest(theta = HR, theta.ci.lb = HR.025, theta.ci.ub = HR.975, 
+                 theta.slab = Study, xlab = "Hazard ratio of HER2 versus OS", refline = 1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘guide.Rnw’ using knitr
Quitting from lines 288-294 (guide.Rnw) 
Error: processing vignette 'guide.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘guide.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxplot.data.frame
> ### Title: Boxplot Method for Data Frame
> ### Aliases: boxplot.data.frame
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(magrittr)
> Theoph %<>% mutate(site = ifelse(as.numeric(Subject) > 6, 'Site A','Site B'))
> boxplot(Theoph,'Subject','conc')
> boxplot(Theoph,Subject,conc)
> boxplot(Theoph,Subject,conc, gg = T)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metaplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crosshairs
> ### Title: Creates a Cross-hairs Plot.
> ### Aliases: cross-hairs crosshairs
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Load and attach metaplotr package to the Global Environment
> ##D library(metaplotr)
> ##D 
> ##D # Remove all variables in the .GlobalEnv, effectively clearing .GlobalEvn
> ##D rm(list = ls())
> ##D 
> ##D # Find out more about the data set from Ferguson and Brannick (2012)
> ##D # help("FergusonBrannick2012")
> ##D 
> ##D # You can check out help file of the \code{crosshairs} function.
> ##D # help(crosshairs)
> ## End(Not run)
> 
> # Basic usage of the \code{crosshairs} function.
> crosshairs(FergusonBrannick2012$pub_z, FergusonBrannick2012$dis_z,
+ FergusonBrannick2012$pub_z_se, FergusonBrannick2012$dis_z_se)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: crosshairs ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_use_crosshairs.Rmd’ using rmarkdown
Quitting from lines 50-51 (how_to_use_crosshairs.Rmd) 
Error: processing vignette 'how_to_use_crosshairs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘how_to_use_crosshairs.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  MatFile.cpp:40:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
  MatFile.cpp:65:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MetaSKAT.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaStan_BNHM.Rmd’ using rmarkdown
Quitting from lines 44-70 (MetaStan_BNHM.Rmd) 
Error: processing vignette 'MetaStan_BNHM.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MetaStan_BNHM.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viz_forest
> ### Title: Forest plot variants for meta-analyses
> ### Aliases: viz_forest
> 
> ### ** Examples
> 
> library(metaviz)
> # Plotting the mozart data using a classic forest plot
> viz_forest(x = mozart[, c("d", "se")],
+ study_labels = mozart[, "study_name"], xlab = "Cohen d")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘funnelinf.Rmd’ using rmarkdown
Quitting from lines 48-49 (funnelinf.Rmd) 
Error: processing vignette 'funnelinf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘funnelinf.Rmd’

--- re-building ‘metaviz.Rmd’ using rmarkdown
Quitting from lines 38-40 (metaviz.Rmd) 
Error: processing vignette 'metaviz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘metaviz.Rmd’

SUMMARY: processing the following files failed:
  ‘funnelinf.Rmd’ ‘metaviz.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: temperatures
> ### Title: Temperature meteogram
> ### Aliases: temperatures
> ### Keywords: temperatures
> 
> ### ** Examples
> 
> data(example_temperature.data)
> temperatures(temperature.data,plot.dewt=TRUE,plot.surf=TRUE,
+ 	plot.min_max=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Methplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotdata
> ### Title: This function visualizes the dataframe yielded by function
> ###   "getdata".
> ### Aliases: plotdata
> 
> ### ** Examples
> 
> data(mydata)
> plotdata(mydata, x.title="Methylation Plot", condition="P1_A1", n=10, legendpos="right")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘metR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ConvertLongitude
> ### Title: Converts between longitude conventions
> ### Aliases: ConvertLongitude
> 
> ### ** Examples
> 
> library(ggplot2)
> library(data.table)
> data(geopotential)
> ggplot(geopotential[date == date[1]], aes(lon, lat, z = gh)) +
+     geom_contour(color = "black") +
+     geom_contour(aes(x = ConvertLongitude(lon)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Visualization-tools.Rmd’ using rmarkdown
Quitting from lines 32-41 (Visualization-tools.Rmd) 
Error: processing vignette 'Visualization-tools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Visualization-tools.Rmd’

--- re-building ‘Working-with-data.Rmd’ using rmarkdown
Quitting from lines 45-50 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Working-with-data.Rmd’

SUMMARY: processing the following files failed:
  ‘Visualization-tools.Rmd’ ‘Working-with-data.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mfbvar_minn
> ### Title: Plotting method for class 'mfbvar_minn'
> ### Aliases: plot.mfbvar_minn
> 
> ### ** Examples
> 
> prior_obj <- set_prior(Y = mf_sweden[, 4:5], freq = c("m", "q"),
+                        n_lags = 4, n_burnin = 20, n_reps = 20, n_fcst = 4)
Warning: prior_Pi_AR1: 0 used as prior mean for AR(1) coefficients.

Warning: lambda1: 0.2 used as the value for the overall tightness hyperparameter.

Warning: lambda2: 1 used as the value for the lag decay hyperparameter.

Warning: lambda3: 10000 used for the constant's prior variance.

> mod_minn <- estimate_mfbvar(prior_obj, prior_type = "minn")
> plot(mod_minn)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Discriminability.Rmd’ using rmarkdown
Quitting from lines 53-55 (Discriminability.Rmd) 
Error: processing vignette 'Discriminability.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Discriminability.Rmd’

--- re-building ‘MGC.Rmd’ using rmarkdown
Quitting from lines 72-73 (MGC.Rmd) 
Error: processing vignette 'MGC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MGC.Rmd’

--- re-building ‘simulations.Rmd’ using rmarkdown
Loading required package: mgc
Loading required package: ggplot2
Quitting from lines 64-69 (simulations.Rmd) 
Error: processing vignette 'simulations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulations.Rmd’

SUMMARY: processing the following files failed:
  ‘Discriminability.Rmd’ ‘MGC.Rmd’ ‘simulations.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check.gamViz
> ### Title: Some diagnostics for a fitted gam model
> ### Aliases: check.gamViz
> 
> ### ** Examples
> 
> library(mgcViz)
> set.seed(0)
> dat <- gamSim(1, n = 200)
Gu & Wahba 4 term additive model
> b <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
> b <- getViz(b)
> 
> # Checks using default options
> check(b)

Method: GCV   Optimizer: magic
Smoothing parameter selection converged after 8 iterations.
The RMS GCV score gradient at convergence was 1.072609e-05 .
The Hessian was positive definite.
Model rank =  37 / 37 

Basis dimension (k) checking results. Low p-value (k-index<1) may
indicate that k is too low, especially if edf is close to k'.

        k'  edf k-index p-value
s(x0) 9.00 2.32    1.00    0.51
s(x1) 9.00 2.31    0.97    0.30
s(x2) 9.00 7.65    0.96    0.27
s(x3) 9.00 1.23    1.04    0.67
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgcviz.rmd’ using rmarkdown
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
Loading required package: qgam
Loading required package: ggplot2
Registered S3 method overwritten by 'mgcViz':
  method from  
  +.gg   GGally

Attaching package: 'mgcViz'

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

    qqline, qqnorm, qqplot

Quitting from lines 66-70 (mgcviz.rmd) 
Error: processing vignette 'mgcviz.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mgcviz.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette1.Rnw’ using knitr
Quitting from lines 59-61 (vignette1.Rnw) 
Error: processing vignette 'vignette1.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette1.Rnw’

SUMMARY: processing the following file failed:
  ‘vignette1.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.microbenchmark
> ### Title: Autoplot method for microbenchmark objects: Prettier graphs for
> ###   microbenchmark using ggplot2
> ### Aliases: autoplot.microbenchmark
> 
> ### ** Examples
> 
> if (requireNamespace("ggplot2")) {
+ 
+ tm <- microbenchmark(rchisq(100, 0),
+                      rchisq(100, 1),
+                      rchisq(100, 2),
+                      rchisq(100, 3),
+                      rchisq(100, 5), times=1000L)
+ ggplot2::autoplot(tm)
+ }
Loading required namespace: ggplot2
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘micromap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmgroupedplot
> ### Title: Linked Micromaps
> ### Aliases: lmgroupedplot lmplot mmgroupedplot mmplot lmplot mmgroupedplot
> ###   lmgroupedplot mmplot.SpatialPolygonsDataFrame mmplot.default
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # initial example
> 
> data("USstates")
> head(USstates@data)
  ST    ST_NAME   AREA_KM  PERIM_KM
0 AK     Alaska 1506038.1 60260.638
1 AL    Alabama  133761.0  2354.600
2 AR   Arkansas  137733.7  2172.208
3 AZ    Arizona  295267.5  2395.409
4 CA California  409603.3  5682.304
5 CO   Colorado  269599.9  2100.092
> statePolys <- create_map_table(USstates, 'ST')
> head(statePolys)
  ID region poly coordsx coordsy hole plotorder plug
1 AK      1    1       2       5    0         1    0
2 AK      1    1       7      10    0         1    0
3 AK      1    1       4      12    0         1    0
4 AK      1    1       7      15    0         1    0
5 AK      1    1       4      15    0         1    0
6 AK      1    1       4      17    0         1    0
> 
> data("edPov")
> 
> # basic figure 1
> lmplot(stat.data = edPov,
+   	map.data = statePolys,
+ 	panel.types = c('labels', 'dot', 'dot','map'),
+ 	panel.data = list('state','pov','ed', NA),
+ 	ord.by = 'pov',   
+ 	grouping = 5, median.row = TRUE,
+ 	map.link = c('StateAb','ID'))
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lmplot -> mmplot -> mmplot.default -> print -> print.mm
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_Guide.Rnw’ using Sweave
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: RColorBrewer
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Coordinate system already present. Adding new coordinate system, which will replace the existing one.

Error: processing vignette 'Introduction_Guide.Rnw' failed with diagnostics:
 chunk 5 (label = fig1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘Introduction_Guide.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_collapse
> ### Title: Set the 'ggplot2' theme to remove all marginal space.
> ### Aliases: theme_collapse
> ### Keywords: ggplot2
> 
> ### ** Examples
> 
> theme_collapse()
List of 61
 $ line                 :List of 6
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ lineend      : chr "butt"
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ rect                 :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ text                 :List of 11
  ..$ family       : chr ""
  ..$ face         : chr "plain"
  ..$ colour       : chr "black"
  ..$ size         : num 11
  ..$ hjust        : num 0.5
  ..$ vjust        : num 0.5
  ..$ angle        : num 0
  ..$ lineheight   : num 0.9
  ..$ margin       :Error in x[[3]] : subscript out of bounds
Calls: <Anonymous> ... format.fun -> format -> format.unit -> vapply -> FUN
Execution halted
Running examples in ‘microsamplingDesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: construct2CompModel
> ### Title: construct a 2 compartmental 'PkModel-class' by providing
> ###   parameters and dosing info
> ### Aliases: construct2CompModel
> 
> ### ** Examples
> 
>   dosingInfo              <-  data.frame( time = 0 , dose = 1 )
>   dataParametersFile      <-  system.file(  "extData",
+  "examplePkParameters.csv" ,   package = "microsamplingDesign" )
>   exampleParameters       <-  read.csv( dataParametersFile ,
+  stringsAsFactors = FALSE , na.strings = NULL )
>   pkModel                 <-  construct2CompModel( exampleParameters , dosingInfo ) 
>   plotObject( pkModel , times = seq( 0, 5 , 0.1) , nSamplesIntegration = 12 )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Loading required package: Rcpp
Quitting from lines 387-392 (microsamplingDesign.Rmd) 
Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘microsamplingDesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
Quitting from lines 634-643 (milr-intro.Rmd) 
Error: processing vignette 'milr-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘milr-intro.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: miranorm
> ### Title: Adaptive algorithm to identify normalization genes.
> ### Aliases: miranorm
> 
> ### ** Examples
> 
> dat = simData(n.trt=15, n.ctrl=15, n.gene=30, n.err=10, sigma.error = c(1, 0.3), mean.sample = 2,
+ sigma.sample = 1.88 , sigma.gene = 0.1, n.big.effect = 5, n.small.effect = 10, mean.big.effect = 2,
+ mean.small.effect = 1.2)$sim
> 
> obj = miranorm(data = dat, group = dat$Group, method="simple")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: miranorm ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘miscset.Rmd’ using rmarkdown
Quitting from lines 117-122 (miscset.Rmd) 
Error: processing vignette 'miscset.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘miscset.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isoplot
> ### Title: plot isotopologues
> ### Aliases: isoplot
> 
> ### ** Examples
> 
> data(lcms)
> explist <- prefilter(lcms, subgroup = c("B", "C", "D"), unlabel = "B")

(1) Checking input parameters...done
(2) Calculating fold change...done
(3) Performing statistical test...done
(4) Performing the first filtering...done> exp.B <- explist$B
> exp.C <- explist$C
> exp.D <- explist$D
> iso.C <- diso(iso1 = 'H2', n11 = 4, n12 = 2, exp.base = exp.B, exp.iso = exp.C)

(1) Checking input parameters...done
(2) Preparing datacube...done
(3) Performing the 2ed filtering...done> iso.D <- diso(iso1 = 'C13', n11 = 9, n12 = 6, iso2 = 'N15', n21 = 1, n22 = 0,
+ exp.base = iso.C[,1:3], exp.iso = exp.D)

(1) Checking input parameters...done
(2) Preparing datacube...done
(3) Performing the 2ed filtering...done> full_result <- Fresult(iso.C, iso.D)
> isoplot(full_result, 1)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: isoplot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘misscompare.Rmd’ using rmarkdown
Quitting from lines 154-155 (misscompare.Rmd) 
Error: processing vignette 'misscompare.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘misscompare.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QQplotgg
> ### Title: Implementation of Quantile-Quantile Plot with ggplot2
> ### Aliases: QQplotgg QQplotgg.default QQplotgg.dist QQnormgg
> 
> ### ** Examples
> 
> # sample vs sample
> QQplotgg(r(normdist(), 10000), r(tdist(df = 4), 10000))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mistr-extensions.Rmd’ using rmarkdown

Attaching package: 'mistr'

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

    q

Quitting from lines 180-184 (mistr-extensions.Rmd) 
Error: processing vignette 'mistr-extensions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mistr-extensions.Rmd’

--- re-building ‘mistr-introduction.Rmd’ using rmarkdown

Attaching package: 'mistr'

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

    q

Quitting from lines 212-214 (mistr-introduction.Rmd) 
Error: processing vignette 'mistr-introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mistr-introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘mistr-extensions.Rmd’ ‘mistr-introduction.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wqs
> ### Title: Histograms of the Weights, Beta1, and WQS using 'ggplot2'
> ### Aliases: plot.wqs
> ### Keywords: wqs
> 
> ### ** Examples
> 
> #Use simulated dataset and set seed for reproducibility.
> data(simdata87)
> set.seed(23456)
> Wa <- estimate.wqs( y = simdata87$y.scenario, X = simdata87$X.true[ , 1:9],
+                   B = 10, family = "binomial")
## No missing values in matrix detected. Regular Quantiles computed.
## No missing values in matrix detected. Regular Quantiles computed.
> plot(Wa, filename = file.path(tempdir(), "WQS_Plot"))
Saving 7 x 7 in image
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘mixR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mixfitEM
> ### Title: Plotting the Fitted Mixture Models
> ### Aliases: plot.mixfitEM
> 
> ### ** Examples
> 
> x <- rmixnormal(200, c(0.3, 0.7), c(2, 5), c(1, 0.7))
> fit <- mixfit(x, ncomp = 2)
> plot(fit)  # base R plotting system
> plot(fit, "ggplot2")  # ggplot2 plotting system
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [17s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Error: plot (@test-plots.R#9)  ───────────────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: plot(sim) at testthat/test-plots.R:9
  2: plot(sim)
  3: print(p1 + theme(legend.position = "none"), vp = vplayout(1, 1))
  4: print.ggplot(p1 + theme(legend.position = "none"), vp = vplayout(1, 1))
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 2 FAILED: 1
  1. Error: plot (@test-plots.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mizer_vignette.Rnw’ using knitr
Quitting from lines 572-573 (mizer_vignette.Rnw) 
Error: processing vignette 'mizer_vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mizer_vignette.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: melt.long
> ### Title: Transform data.frame to Long Form
> ### Aliases: melt.long
> ### Keywords: univar
> 
> ### ** Examples
> 
> library(ggplot2)
> ## some random data
> test <- data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10))
> test.long <- melt.long(test)
> test.long
          value variable
x1  -0.62645381        x
x2   0.18364332        x
x3  -0.83562861        x
x4   1.59528080        x
x5   0.32950777        x
x6  -0.82046838        x
x7   0.48742905        x
x8   0.73832471        x
x9   0.57578135        x
x10 -0.30538839        x
y1   1.51178117        y
y2   0.38984324        y
y3  -0.62124058        y
y4  -2.21469989        y
y5   1.12493092        y
y6  -0.04493361        y
y7  -0.01619026        y
y8   0.94383621        y
y9   0.82122120        y
y10  0.59390132        y
z1   0.91897737        z
z2   0.78213630        z
z3   0.07456498        z
z4  -1.98935170        z
z5   0.61982575        z
z6  -0.05612874        z
z7  -0.15579551        z
z8  -1.47075238        z
z9  -0.47815006        z
z10  0.41794156        z
> ggplot(test.long, aes(x = variable, y = value)) +
+   geom_boxplot(aes(fill = variable))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKmisc.Rmd’ using rmarkdown
Quitting from lines 123-125 (MKmisc.Rmd) 
Error: processing vignette 'MKmisc.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MKmisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_automation.Rmd’ using rmarkdown
--- finished re-building ‘data_automation.Rmd’

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

--- re-building ‘pitch_plotting.Rmd’ using rmarkdown
Quitting from lines 39-46 (pitch_plotting.Rmd) 
Error: processing vignette 'pitch_plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pitch_plotting.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlrMBO.Rmd’ using rmarkdown
Quitting from lines 63-67 (mlrMBO.Rmd) 
Error: processing vignette 'mlrMBO.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mlrMBO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLZ.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 54-55 (MLZ.Rmd) 
Error: processing vignette 'MLZ.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MLZ.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘modcmfitrOverview.Rmd’ using rmarkdown
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette 'modcmfitrOverview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘modcmfitrOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘model4you-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binomial_glm_plot
> ### Title: Plot for a given logistic regression model (glm with binomial
> ###   family) with one binary covariate.
> ### Aliases: binomial_glm_plot
> 
> ### ** Examples
> 
> set.seed(2017)
> 
> # number of observations
> n <- 1000
> 
> # balanced binary treatment
> # trt <- factor(rep(c("C", "A"), each = n/2),
> #               levels = c("C", "A"))
> 
> # unbalanced binary treatment
> trt <- factor(c(rep("C", n/4), rep("A", 3*n/4)),
+               levels = c("C", "A"))
> 
> # some continuous variables
> x1 <- rnorm(n)
> x2 <- rnorm(n)
> 
> # linear predictor
> lp <- -0.5 + 0.5*I(trt == "A") + 1*I(trt == "A")*I(x1 > 0)
> 
> # compute probability with inverse logit function
> invlogit <- function(x) 1/(1 + exp(-x))
> pr <- invlogit(lp)
> 
> # bernoulli response variable
> y <- rbinom(n, 1, pr)
> dat <- data.frame(y, trt, x1, x2)
> 
> # logistic regression model
> mod <- glm(y ~ trt, data = dat, family = "binomial")
> binomial_glm_plot(mod, plot_data = TRUE)
Warning: Ignoring unknown aesthetics: width
Warning: Using alpha for a discrete variable is not advised.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘modeldb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_kmeans
> ### Title: Visualize a KMeans Cluster with lots of data
> ### Aliases: plot_kmeans db_calculate_squares
> 
> ### ** Examples
> 
> plot_kmeans(mtcars, mpg, wt, group = am)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ModelGood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Ctree
> ### Title: S3 wrapper function for party's ctree method
> ### Aliases: Ctree
> 
> ### ** Examples
> 
> library(party)
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
> set.seed(7)
> x <- abs(rnorm(20))
> d <- data.frame(y=rbinom(20,1,x/max(x)),x=x,z=rnorm(20))
> ct <- Ctree(y~x+z,d)
> plot(ct$ctree)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Running examples in ‘moderndive-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bowl
> ### Title: A sampling bowl of red and white balls
> ### Aliases: bowl
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(ggplot2)
> 
> # Take 10 different samples of size n = 50 balls from bowl
> bowl_samples_simulated <- bowl %>%
+   rep_sample_n(50, reps = 10)
>   
> # Compute 10 different p_hats (prop red) based on 10 different samples of
> # size n = 50
> p_hats <- bowl_samples_simulated %>%
+   group_by(replicate, color) %>%
+   summarize(count = n()) %>%
+   mutate(proportion = count/50) %>%
+   filter(color == "red")
> 
> # Plot sampling distribution
> ggplot(p_hats, aes(x = proportion)) +
+   geom_histogram(binwidth = 0.05) +
+   labs(x = expression(hat(p)), y = "Number of samples", 
+   title = "Sampling distribution of p_hat based 10 samples of size n = 50")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_Usage.Rmd’ using rmarkdown
--- finished re-building ‘Basic_Usage.Rmd’

--- re-building ‘Comparison_Usage.Rmd’ using rmarkdown
Quitting from lines 243-278 (Comparison_Usage.Rmd) 
Error: processing vignette 'Comparison_Usage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Comparison_Usage.Rmd’

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

--- re-building ‘problem-definition.Rmd’ using rmarkdown
--- finished re-building ‘problem-definition.Rmd’

--- re-building ‘writing-functions-for-moeadr.Rmd’ using rmarkdown
--- finished re-building ‘writing-functions-for-moeadr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpatialCov
> ### Title: Plot observations on raster image
> ### Aliases: plotSpatialCov
> 
> ### ** Examples
> 
> stepDist <- "gamma"
> angleDist <- "vm"
> 
> # plot simulated data over forest raster automatically loaded with the packge
> spatialCov<-list(forest=forest)
> data <- simData(nbAnimals=2,nbStates=2,dist=list(step=stepDist,angle=angleDist),
+                 Par=list(step=c(100,1000,50,100),angle=c(0,0,0.1,5)),
+                 beta=matrix(c(5,-10,-25,50),nrow=2,ncol=2,byrow=TRUE),
+                 formula=~forest,spatialCovs=spatialCov,
+                 obsPerAnimal=225,states=TRUE)
=======================================================================
Simulating HMM with 2 states and 2 data streams
-----------------------------------------------------------------------

 step ~ gamma(mean=~1, sd=~1)
 angle ~ vm(mean=~1, concentration=~1)

 Transition probability matrix formula: ~forest

 Initial distribution formula: ~1
=======================================================================
DONE
> 
> plotSpatialCov(data,forest,states=data$states)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotSpatialCov ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Momocs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCcontrib
> ### Title: Shape variation along PC axes
> ### Aliases: PCcontrib PCcontrib.PCA
> 
> ### ** Examples
> 
> bot.p <- PCA(efourier(bot, 12))
you selected `norm=TRUE`, which is not recommended. See ?efourier
> PCcontrib(bot.p)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: PCcontrib ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
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-patched-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [51s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ────────────────
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  ── 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ────────────────
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  ── 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ────────────────
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  ── 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ────────────────
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  ── 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ────────────────
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 315 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MonteCarlo-Vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 316-320 (MonteCarlo-Vignette.Rmd) 
Error: processing vignette 'MonteCarlo-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MonteCarlo-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MonteCarlo-Vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reproData
> ### Title: Plotting method for 'reproData' objects
> ### Aliases: plot.reproData
> ### Keywords: plot
> 
> ### ** Examples
> 
> # (1) Load the data
> data(cadmium1)
> 
> # (2) Create an object of class 'reproData'
> cadmium1 <- reproData(cadmium1)
> 
> # (3) Plot the reproduction data
> plot(cadmium1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mortAAR_vignette-1.Rmd’ using rmarkdown
Loading required package: bitops
Quitting from lines 131-132 (mortAAR_vignette-1.Rmd) 
Error: processing vignette 'mortAAR_vignette-1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mortAAR_vignette-1.Rmd’

--- re-building ‘mortAAR_vignette_extended.Rmd’ using rmarkdown
Loading required package: bitops
Quitting from lines 146-148 (mortAAR_vignette_extended.Rmd) 
Error: processing vignette 'mortAAR_vignette_extended.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mortAAR_vignette_extended.Rmd’

SUMMARY: processing the following files failed:
  ‘mortAAR_vignette-1.Rmd’ ‘mortAAR_vignette_extended.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCohortTable
> ### Title: Return the cohort life table as a 'mortalityTable.period' object
> ### Aliases: getCohortTable getCohortTable,mortalityTable-method
> 
> ### ** Examples
> 
> mortalityTables.load("Austria_Annuities")
Loading table dataset 'Austria_Annuities'
Loading table dataset 'Austria_Annuities_AVOe1996R'
Loading table dataset 'Austria_Annuities_AVOe2005R'
Loading table dataset 'Austria_Annuities_EROMF'
Loading table dataset 'Austria_Annuities_RR67'
> tb75 = getCohortTable(AVOe2005R.male, YOB = 1975)
> # The tb75 is a fixed table with no trend any more
> plot(AVOe2005R.male, tb75, Period = 2017)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: scales
Quitting from lines 122-131 (using-the-mortalityTables-package.Rmd) 
Error: processing vignette 'using-the-mortalityTables-package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following file failed:
  ‘using-the-mortalityTables-package.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Houses_for_sale
> ### Title: Houses for sale
> ### Aliases: Houses_for_sale
> ### Keywords: datasets
> 
> ### ** Examples
> 
> mod_1 <- lm(price ~ fireplaces, data = Houses_for_sale)
> mod_2 <- lm(price ~ fireplaces + living_area, data = Houses_for_sale)
> mod_effect(mod_1, ~ fireplaces)
     slope fireplaces to_fireplaces
1 66698.82          1           1.4
> mod_effect(mod_2, ~ fireplaces)
    slope fireplaces to_fireplaces living_area
1 8962.44          1           1.4        1600
> mod_plot(mod_2, ~ living_area + fireplaces)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basics.Rmd’ using rmarkdown
Quitting from lines 66-68 (Basics.Rmd) 
Error: processing vignette 'Basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CIsim
> ### Title: Compute confidence intervals from (multiple) simulated data sets
> ### Aliases: CIsim
> ### Keywords: inference simulation
> 
> ### ** Examples
> 
> # 1000 95% intervals using t.test; population is N(0,1)
> CIsim(n=10, samples=1000)    
Interval coverage:
    cover
n      Low   Yes  High
  10 0.019 0.957 0.024
> # this time population is Exp(1); fewer samples, so we get a plot 
> CIsim(n=10, samples=100, rdist=rexp, estimand=1) 
Interval coverage:
    cover
n     Low  Yes High
  10 0.04 0.96 0.00
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: CIsim ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘motoRneuron.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: dygraphs
Quitting from lines 121-122 (motoRneuron.Rmd) 
Error: processing vignette 'motoRneuron.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘motoRneuron.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bezier
> ### Title: Create Bezier-curves using the Bernstein approximation.
> ### Aliases: bezier
> 
> ### ** Examples
> 
> # Generate range of Bezier-curves
> bezier_curves <- bezier(w=seq(0,10,.1))
> 
> # Plot curves
> mt_plot(bezier_curves)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘browseMovebank.Rnw’ using Sweave
--- finished re-building ‘browseMovebank.Rnw’

--- re-building ‘move.Rnw’ using Sweave
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Loading required package: ggplot2
Google's Terms of Service: https://cloud.google.com/maps-platform/terms/.
Please cite ggmap if you use it! See citation("ggmap") for details.
Loading required package: mapproj
Loading required package: maps
Error: processing vignette 'move.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘move.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave
trying URL ‘https://datacube.wu.ac.at/src/contrib/corpus.useR.2008.abstracts_2009.08.10.tar.gz’
Content type 'application/x-gzip' length 98736 bytes (96 KB)
==================================================
downloaded 96 KB

* installing *source* package ‘corpus.useR.2008.abstracts’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (corpus.useR.2008.abstracts)

The downloaded source packages are in
	'/tmp/RtmpDz24vJ/downloaded_packages'
Loading required package: NLP

Error: processing vignette 'movMF.Rnw' failed with diagnostics:
 chunk 18 
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'movMF.Rnw'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: af
> ### Title: The adaptive fence procedure
> ### Aliases: af
> 
> ### ** Examples
> 
> n = 100
> set.seed(11)
> e = rnorm(n)
> x1 = rnorm(n)
> x2 = rnorm(n)
> x3 = x1^2
> x4 = x2^2
> x5 = x1*x2
> y = 1 + x1 + x2 + e
> dat = data.frame(y,x1,x2,x3,x4,x5)
> lm1 = lm(y ~ ., data = dat)
> ## Don't show: 
> af1 = af(lm1, cores = 1, B = 5, n.c = 5, seed = 1)
> summary(af1)

Call:
af(mf = lm1, B = 5, n.c = 5, cores = 1, seed = 1)

Adaptive fence model (c*=17.9):
y ~ x1 + x2

Model sizes considered: 1 to 7 (including intercept).

> plot(af1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mpoly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.mpoly
> ### Title: Convert an object to an mpoly
> ### Aliases: as.mpoly
> 
> ### ** Examples
> 
> 
> library(ggplot2); theme_set(theme_classic())

Attaching package: ‘ggplot2’

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

    vars

> library(dplyr)

Attaching package: ‘dplyr’

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

    vars

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> n <- 101
> s <- seq(-5, 5, length.out = n)
> 
> 
> 
> # one dimensional case
> 
> df <- data.frame(x = seq(-5, 5, length.out = n)) %>% 
+   mutate(y = -x^2 + 2*x - 3 + rnorm(n, 0, 2))
> 
> (mod <- lm(y ~ x + I(x^2), data = df))

Call:
lm(formula = y ~ x + I(x^2), data = df)

Coefficients:
(Intercept)            x       I(x^2)  
     -2.709        1.983       -1.010  

> (p <- as.mpoly(mod))
1.98275 x  -  1.010312 x^2  -  2.709013> qplot(x, y, data = df) +
+   stat_function(fun = as.function(p), colour = "red", size = 1)
f(.) with . = x
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mppR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mpp_CIM
> ### Title: MPP Composite Interval Mapping
> ### Aliases: mpp_CIM
> 
> ### ** Examples
> 
> 
> # Cross-specific effect model
> #############################
> 
> data(mppData)
> 
> SIM <- mpp_SIM(mppData = mppData, Q.eff = "cr")
> 
> cofactors <- QTL_select(Qprof = SIM, threshold = 3, window = 20)
> 
> CIM <- mpp_CIM(mppData = mppData, Q.eff = "cr", cofactors = cofactors,
+                window = 20, plot.gen.eff = TRUE)
> 
> plot(x = CIM)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mppR_vignette.rnw’ using Sweave

Error: processing vignette 'mppR_vignette.rnw' failed with diagnostics:
 chunk 15 (label = mpp_proc) 
Error in Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘mppR_vignette.rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-bayen_kuhlmann_2011.rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 220-221 (introduction-bayen_kuhlmann_2011.rmd) 
Error: processing vignette 'introduction-bayen_kuhlmann_2011.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-bayen_kuhlmann_2011.rmd’

SUMMARY: processing the following file failed:
  ‘introduction-bayen_kuhlmann_2011.rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMRF_hm
> ### Title: Plot MRF interaction parameters as a heatmap
> ### Aliases: plotMRF_hm
> 
> ### ** Examples
> 
> 
> data("Bird.parasites")
> CRFmod <- MRFcov(data = Bird.parasites, n_nodes = 4, family = 'binomial')
Leave-one-out cv used for the following low-occurrence (rare) nodes:
 Microfilaria ...
Fitting MRF models in sequence using 1 core ...
> plotMRF_hm(MRF_mod = CRFmod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bird_Parasite_CRF.Rmd’ using rmarkdown
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Welcome to MRFcov. If you use the package, please cite as: Clark, NJ, Wells, K and Lindberg, O. 2018. Unravelling changing interspecific interactions across environmental gradients using Markov random fields. Ecology doi: 10.1002/ecy.2221 
Quitting from lines 44-47 (Bird_Parasite_CRF.Rmd) 
Error: processing vignette 'Bird_Parasite_CRF.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Bird_Parasite_CRF.Rmd’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bagplot
> ### Title: Draws a bagplot, a bivariate boxplot
> ### Aliases: bagplot
> ### Keywords: Graphical
> 
> ### ** Examples
> 
> data(bloodfat)
> 
> # The bagplot can be plotted for the halfspace depth,
> # the projection depth or the skewness-adjusted projection depth.
> # Note that the projection depth is not appropiate for skewed data.
> bagplot(compBagplot(bloodfat))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘MRPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DendroModuleGraph 
> ### Title: Visualization of Nodes by Dendrogram with Modules and Inferred
> ###   Graph
> ### Aliases: 'DendroModuleGraph '
> 
> ### ** Examples
> 
> 
> # Adjacency matrix from directed example graph
> Adj_directed <- as(ExampleMRPC$complex$cont$withGV$graph,
+                    "matrix")
> 
> # Plot of the graph
> DendroModuleGraph(Adj_directed,
+                   minModuleSize = 5,
+                   GV = 14)
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..cutHeight not given, setting it to 0.975  ===>  99% of the (truncated) height range in dendro.
 ..done.
$graph
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CheckingSynth.Rmd’ using rmarkdown
--- finished re-building ‘CheckingSynth.Rmd’

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

--- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown
Quitting from lines 154-156 (WorkingWithMSCMT.Rmd) 
Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘WorkingWithMSCMT.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
> data(canabalt)
> print(qplot(device, score, data = canabalt))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘MSPRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: implement.MSPRT
> ### Title: Implementing a MSPRT
> ### Aliases: implement.MSPRT
> 
> ### ** Examples
> 
> 
> # the termination thresholds are obtained from design.MSPRT()
> 
> ## one-sample tests
> 
> ### proportion test
> 
> x = c(0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0,
+       0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0)
> 
> implement.MSPRT(obs = x, test.type = "oneProp", null = 0.2,
+                 term.thresh = 22.63, N.max = 30)
[1] "-------------------------------------------------------------------------"
[1] "Implementing the MSPRT in case of a one-sample binomial proportion test:"
[1] "-------------------------------------------------------------------------"
[1] "Working with side = right (default)"
[1] "             batch.seq = 1:N.max (default)"
[1] "             type1 = 0.005 (default)"
[1] "             type2 = 0.2 (default)"
[1] "             null = 0.2 (user specified)"
[1] "Required parameters are taken care of!"
[1] "-------------------------------------------------------------------------"
[1] "The UMPBT alternative has been obtained: 0.367 & 0.4 with probabilities 0.296 & 0.704, respectively"
[1] "-------------------------------------------------------------------------"
[1] "Sequential comparison done!"
[1] "-------------------------------------------------------------------------"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: implement.MSPRT
Execution halted
Running examples in ‘MST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
> 
> (tree_final <- getTree(fit, 4))

Model formula:
Surv(time, status) ~ x1 + x2 + x3 + x4 + id

Fitted party:
[1] root
|   [2] x2 > 0.3
|   |   [3] x1 > 0.5: 1.694 (n = 208)
|   |   [4] x1 <= 0.5: 0.702 (n = 292)
|   [5] x2 <= 0.3
|   |   [6] x1 > 0.5: 0.977 (n = 112)
|   |   [7] x1 <= 0.5: 0.334 (n = 188)

Number of inner nodes:    3
Number of terminal nodes: 4
> plot(tree_final)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘create_mtc_device.Rmd’ using rmarkdown
--- finished re-building 'create_mtc_device.Rmd'

--- re-building ‘simulate_map_gcode.Rmd’ using rmarkdown
Quitting from lines 65-73 (simulate_map_gcode.Rmd) 
Error: processing vignette 'simulate_map_gcode.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'simulate_map_gcode.Rmd'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mtlr
> ### Title: Graphical Representation of Feature Weights
> ### Aliases: plot.mtlr
> 
> ### ** Examples
> 
> #These examples are geared towards users who have installed ggplot2 and reshape2.
> library(survival)
> mod <- mtlr(Surv(time,status)~., data = lung)
> #Basic plot with 5 most influential features
> plot(mod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘workflow.Rmd’ using rmarkdown
Quitting from lines 115-116 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘mudata2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alta_lake
> ### Title: Alta Lake Gravity Core Data
> ### Aliases: alta_lake
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> autoplot(alta_lake, y = "depth") + scale_y_reverse()
Using x = "value"
Using first 9 facets of 14. Use max_facets = FALSE to plot all facets
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mudata.Rmd’ using rmarkdown
Warning: Removed 112 rows containing missing values (geom_path).
Quitting from lines 70-71 (mudata.Rmd) 
Error: processing vignette 'mudata.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mudata.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HVT
> ### Title: Constructing Hierarchical Voronoi Tessellations
> ### Aliases: HVT
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(USArrests)
> hvt.results <- list()
> hvt.results <- HVT(USArrests, nclust = 6, depth = 1, quant.err = 0.2, 
+                   projection.scale = 10, normalize = TRUE)
Loading required namespace: MASS
Loading required namespace: deldir
Loading required namespace: Hmisc
Loading required namespace: splancs
Loading required namespace: conf.design

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


> plotHVT(hvt.results, line.width = c(0.8), color.vec = c('#141B41'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SIR-MCMC.Rmd’ using rmarkdown
Quitting from lines 121-130 (SIR-MCMC.Rmd) 
Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SIR-MCMC.Rmd’

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

SUMMARY: processing the following file failed:
  ‘SIR-MCMC.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxWhisker
> ### Title: A function to create a box and whisker plot by group ID
> ### Aliases: boxWhisker
> 
> ### ** Examples
> 
> data(Nuclei)
> data(Groups)
> boxWhisker(Nuclei, Groups)
Warning: Removed 98 rows containing non-finite values (stat_boxplot).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘multipanelfigure-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: billing2016_suppfig4e
> ### Title: Mass spectrometry intensities by stem cell type and organelle
> ### Aliases: billing2016_suppfig4e
> 
> ### ** Examples
> 
> ggplot2::ggplot(billing2016_suppfig4e, ggplot2::aes(Experiment, Intensity)) +
+   ggplot2::geom_bar(stat = "identity") +
+   ggplot2::geom_vline(xintercept = seq(3.5, 24.5, 3), linetype = "dotted") +
+   ggplot2::facet_wrap(~ GeneName) +
+   ggplot2::xlab(NULL) +
+   ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size = 4))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘munsell-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chroma_slice
> ### Title: Plot all colours with the same chroma
> ### Aliases: chroma_slice
> 
> ### ** Examples
> 
> chroma_slice(2)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_musica.Rmd’ using rmarkdown
Quitting from lines 64-67 (using_musica.Rmd) 
Error: processing vignette 'using_musica.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_musica.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSignatureExposures
> ### Title: Generate Plot Signature
> ### Aliases: plotSignatureExposures
> 
> ### ** Examples
> 
> tmp <- getTestRunArgs(6)
> gp <- plotSignatureExposures(tmp)
> gp + ggtitle("de novo mutSignatures")  + scale_fill_manual(values = c("#377eb8", "#4daf4a"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mvdalab-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVComp
> ### Title: Traditional Multivariate Mean Vector Comparison
> ### Aliases: MVComp print.mvcomp
> 
> ### ** Examples
> 
> data(College)
> dat1 <- College
> #Generate a 'fake' difference of 15 units
> dat2 <- College + matrix(rnorm(nrow(dat1) * ncol(dat1), mean = 15), 
+         nrow = nrow(dat1), ncol = ncol(dat1))
> 
> Comparison <- MVComp(dat1, dat2, level = .95)
> Comparison
  lower 95 % confidence upper 95 % confidence    Significance
1             -47.95688              17.74004 Not Significant
2             -19.78226             -10.13067     Significant
3             -17.15396             -12.86984     Significant
> plot(Comparison, Diff2Plot = c(1, 2), include.zero = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘mwaved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiCoef
> ### Title: Wavelet coefficient estimation from a multichannel signal
> ### Aliases: multiCoef
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m*n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25,m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10,15,20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> plot(signal, type='l', lty='dashed', main='dashed: True signal, solid: multichannel signals')
> matlines(Y, lty = 1)
> # Estimate the wavelet coefficients
> estimatedCoefs <- multiCoef(Y, G, alpha = alpha)
> plot(estimatedCoefs)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mWaveD.Rmd’ using rmarkdown
Quitting from lines 196-215 (mWaveD.Rmd) 
Error: processing vignette 'mWaveD.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mWaveD.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotContribution
> ### Title: Plot Cumuative Transcriptome Index
> ### Aliases: PlotContribution
> 
> ### ** Examples
> 
> 
>  data(PhyloExpressionSetExample)
>  data(DivergenceExpressionSetExample)
>  
>  # visualize phylostratum contribution to global TAI
>  PlotContribution(PhyloExpressionSetExample, legendName = "PS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced.Rmd’ using rmarkdown
--- finished re-building ‘Advanced.Rmd’

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

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

--- re-building ‘Intermediate.Rmd’ using rmarkdown
Quitting from lines 87-91 (Intermediate.Rmd) 
Error: processing vignette 'Intermediate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intermediate.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 413-421 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

SUMMARY: processing the following files failed:
  ‘Intermediate.Rmd’ ‘Introduction.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: matrix_raster_plot
> ### Title: Make a raster plot of a matrix.
> ### Aliases: matrix_raster_plot
> 
> ### ** Examples
> 
> img <- ijtiff::read_tif(system.file('extdata', '50.tif', package = 'nandb'))
Reading 50.tif: an 8-bit, 50x50 pixel image of unsigned
integer type with 1 channel and 50 frames . . .
 Done.
> ijtiff::display(img[, , 1, 1])
> matrix_raster_plot(img[, , 1, 1])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.Rmd’ using rmarkdown
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘brightness-timeseries.Rmd’ using rmarkdown
--- finished re-building ‘brightness-timeseries.Rmd’

--- re-building ‘single-images.Rmd’ using rmarkdown
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Quitting from lines 52-70 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
  ‘single-images.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(naniar)
  > 
  > test_check("naniar")
  ── 1. Error: (unknown) (@test-gg_miss_upset.R#3)  ──────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: gg_miss_upset(riskfactors) at testthat/test-gg_miss_upset.R:3
  2: data %>% as_shadow_upset() %>% UpSetR::upset(order.by = order.by, ...)
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: withVisible(function_list[[k]](value))
  9: function_list[[k]](value)
  10: UpSetR::upset(., order.by = order.by, ...)
  ...
  36: pushvpgp(x)
  37: pushgrobvp(x$vp)
  38: pushgrobvp.viewport(x$vp)
  39: pushViewport(vp, recording = FALSE)
  40: lapply(vps, push.vp, recording)
  41: FUN(X[[i]], ...)
  42: push.vp.vpTree(X[[i]], ...)
  43: push.vp(vp$parent, recording)
  44: push.vp.viewport(vp$parent, recording)
  45: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 470 SKIPPED: 22 FAILED: 1
  1. Error: (unknown) (@test-gg_miss_upset.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 92-100 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Quitting from lines 64-67 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
Quitting from lines 29-32 (naniar-visualisation.Rmd) 
Error: processing vignette 'naniar-visualisation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
--- finished re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘naniar-visualisation.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plot Method for the 'nblda' and 'nblda_trained' Classes
> ### Aliases: plot plot.nblda plot.nblda_trained plot,nblda-method
> ###   plot,nblda_trained-method
> 
> ### ** Examples
> 
> set.seed(2128)
> counts <- generateCountData(n = 20, p = 10, K = 2, param = 1, sdsignal = 0.5,
+                             DE = 0.8, allZero.rm = FALSE, tag.samples = TRUE)
> x <- t(counts$x + 1)
> y <- counts$y
> xte <- t(counts$xte + 1)
> ctrl <- nbldaControl(folds = 2, repeats = 2)
> 
> fit <- trainNBLDA(x = x, y = y, type = "mle", tuneLength = 10,
+                   metric = "accuracy", train.control = ctrl)
Warning in nblda(x = x, y = y, xte = NULL, rhos = best.rho, beta = tc$beta,  :
  Since no xte was provided, testing was performed on training data set.
> 
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ncappc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ncappc
> ### Title: Performs NCA calculations and population PK model diagnosis.
> ### Aliases: ncappc
> 
> ### ** Examples
> 
> out <- ncappc(obsFile=system.file("extdata","pkdata.csv",package="ncappc"), 
+   onlyNCA = TRUE,
+   extrapolate = TRUE,
+   printOut = FALSE,
+   evid = FALSE,
+   psnOut=FALSE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ncappc ... dv_vs_idv -> dv.plot -> suppressMessages -> withCallingHandlers
Execution halted
Running examples in ‘NeatMap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NeatMap-package
> ### Title: Non-clustered Heatmaps
> ### Aliases: NeatMap-package NeatMap
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> #heatmap1 using pca (the scale_x_continuous ensures that labels can be seen)
> make.heatmap1(mtcars,row.method="PCA",column.method="average.linkage",
+ row.labels=rownames(mtcars),column.labels=colnames(mtcars))+
+ scale_x_continuous(lim=c(-1,15))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘neatmaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: consClustResTable
> ### Title: Consensus Cluster Results in a Table
> ### Aliases: consClustResTable
> 
> ### ** Examples
> 
> # create the data frame using the network, node and edge attributes
> df <- netsDataFrame(network_attr_df,
+                     node_attr_df,
+                     edge_df)
> 
> # run the neatmap code on df
> neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, 
+                     xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: neatmap ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Running examples in ‘netjack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diff_test_ggPlot
> ### Title: Difference Test Plots
> ### Aliases: diff_test_ggPlot
> 
> ### ** Examples
> 
> data(GroupA)
> GroupA_Net = as_NetSample(GroupA, 1:20, node.variables = list(community = c(rep(1, 10), rep(2,10))),
+   sample.variables = list(group = c(rep(1, 10), rep(2,10))))
> Jackknife_GroupA_Net = net_apply(GroupA_Net, node_jackknife)
> GlobEff_GroupA_Net = net_stat_apply(Jackknife_GroupA_Net, global_efficiency)
> diff_test_ggPlot(GlobEff_GroupA_Net)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘developingNetjack.Rmd’ using rmarkdown
--- finished re-building ‘developingNetjack.Rmd’

--- re-building ‘netjackIntro.Rmd’ using rmarkdown
Quitting from lines 147-156 (netjackIntro.Rmd) 
Error: processing vignette 'netjackIntro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘netjackIntro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 73-74 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘VignetteNetworkExt.Rmd’ using rmarkdown
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.


Attaching package: 'NetworkExtinction'

The following object is masked _by_ '.GlobalEnv':

    net

Quitting from lines 129-133 (VignetteNetworkExt.Rmd) 
Error: processing vignette 'VignetteNetworkExt.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘VignetteNetworkExt.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cascade
> ### Title: Plot a cascade object
> ### Aliases: plot.cascade
> 
> ### ** Examples
> 
> 
> data(cascades)
> plot(cascades, selection = names(cascades$cascade_nodes)[1:5])
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart_vignette.Rmd’ using rmarkdown
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.

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

--- re-building ‘tutorial_vignette.Rmd’ using rmarkdown
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.


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 188-190 (tutorial_vignette.Rmd) 
Error: processing vignette 'tutorial_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘network_scaleup.Rmd’ using docco_linear
Loading required package: plyr
Loading required package: dplyr

Attaching package: 'dplyr'

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

    arrange, count, desc, failwith, id, mutate, rename, summarise,
    summarize

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: functional
Loading required package: stringr
Quitting from lines 221-222 (network_scaleup.Rmd) 
Error: processing vignette 'network_scaleup.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘network_scaleup.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: garson
> ### Title: Variable importance using Garson's algorithm
> ### Aliases: garson garson.default garson.numeric garson.nnet garson.mlp
> ###   garson.nn garson.train
> 
> ### ** Examples
> 
> 
> ## using numeric input
> 
> wts_in <- c(13.12, 1.49, 0.16, -0.11, -0.19, -0.16, 0.56, -0.52, 0.81)
> struct <- c(2, 2, 1) #two inputs, two hidden, one output 
> 
> garson(wts_in, struct)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘neurobase.Rmd’ using rmarkdown
--- finished re-building ‘neurobase.Rmd’

--- re-building ‘nifti_basics.Rmd’ using rmarkdown
Quitting from lines 524-527 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nifti_basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess
> ### Title: Compare a given score to a parent population.
> ### Aliases: assess
> 
> ### ** Examples
> 
> require(neuropsychology)
> 
> assess(3.4, mean=2.5, sd=1.2)
[1] "The participant (score = 3.4) is positioned at 0.75 standard deviations from the mean (M = 2.5, SD = 1.2). The participant's score is greater than 77.37 % of the general population."
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘neutralitytestr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lsq_plot
> ### Title: Plot cumulative distribution 'lsq_plot' Plots the cumulative
> ###   distribution of the data as well as the best fit linear model line.
> ### Aliases: lsq_plot
> 
> ### ** Examples
> 
> lsq_plot(neutralitytest(VAFselection, fmin = 0.1, fmax = 0.25))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(neutralitytestr)
  > 
  > test_check("neutralitytestr")
  ── 1. Error: neutralitytest returns correct object (@test_plots.R#5)  ──────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(plot_all(neutralitytest(VAFneutral)), "ggplot") at testthat/test_plots.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: plot_all(neutralitytest(VAFneutral))
  5: cowplot::plot_grid(p1, p2, p3, labels = c("A", "B", "C"), ncol = 3)
  6: align_plots(plotlist = plots, align = align, axis = axis)
  7: lapply(plots, function(x) {
         if (!is.null(x)) 
             plot_to_gtable(x)
         else NULL
     })
  8: FUN(X[[i]], ...)
  9: plot_to_gtable(x)
  10: ggplot2::ggplotGrob(plot)
  ...
  24: pushvpgp(x)
  25: pushgrobvp(x$vp)
  26: pushgrobvp.viewport(x$vp)
  27: pushViewport(vp, recording = FALSE)
  28: lapply(vps, push.vp, recording)
  29: FUN(X[[i]], ...)
  30: push.vp.vpTree(X[[i]], ...)
  31: push.vp(vp$parent, recording)
  32: push.vp.viewport(vp$parent, recording)
  33: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Error: neutralitytest returns correct object (@test_plots.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘neutraltytestr.Rmd’ using rmarkdown
Warning: Removed 2 rows containing missing values (geom_bar).
Quitting from lines 61-62 (neutraltytestr.Rmd) 
Error: processing vignette 'neutraltytestr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘neutraltytestr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).
--- finished re-building ‘demo.Rmd’

--- re-building ‘flow.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).

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

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Quitting from lines 29-34 (flow.Rmd) 
Error: processing vignette 'flow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘flow.Rmd’

--- re-building ‘network.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).

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

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Warning in st_centroid.sf(mendota_lake) :
  st_centroid assumes attributes are constant over geometries of x
Warning in st_centroid.sfc(st_geometry(x), of_largest_polygon = of_largest_polygon) :
  st_centroid does not give correct centroids for longitude/latitude data
Quitting from lines 54-59 (network.Rmd) 
Error: processing vignette 'network.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘network.Rmd’

SUMMARY: processing the following files failed:
  ‘flow.Rmd’ ‘network.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.NHEMOtree
> ### Title: Plot Method for Class NHEMOtree
> ### Aliases: plot.NHEMOtree
> ### Keywords: Plots for NHEMOtree Multi-objective optimization Evolutionary
> ###   algorithms Classification
> 
> ### ** Examples
> 
> # Simulation of data and costs
>   d         <- Sim_Data(Obs=200)
>   CostMatrix<- Sim_Costs()
> 
>   res<- NHEMOtree(type="NHEMO", formula=Y2~., data=d, CostMatrix=CostMatrix, 
+                   gens=5, popsize=5, crossover_prob=0.1, mutation_prob=0.1)
>   plot(data=d, x=res, which="P")
>   plot(data=d, x=res, which="S", col=3, type="l")
>   plot(data=d, x=res, which="V", vim=5)
>   plot(data=d, x=res, which="T")
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Running examples in ‘nhstplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotchisqtest
> ### Title: Illustrate a Chi-Squared Test graphically.
> ### Aliases: plotchisqtest
> 
> ### ** Examples
> 
> #Making a chi-squared plot with Chi-squared of 8 and df of 4
> plotchisqtest(chisq = 8, df = 4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nhstplot.Rmd’ using rmarkdown
Quitting from lines 44-45 (nhstplot.Rmd) 
Error: processing vignette 'nhstplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nhstplot.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmPlots_gg
> ### Title: Linear Model Diagnostic Plots with ggplot2
> ### Aliases: lmPlots_gg
> 
> ### ** Examples
> 
> n <- 100; x1 <- rnorm(n); y1 <- rnorm(n);
> linmod <- lm(y1 ~ x1)
> lmPlots_gg(linmod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lmPlots_gg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘NIRStat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAUCtest
> ### Title: MAUC statistics based Analysis for NIRS time series.
> ### Aliases: MAUCtest
> 
> ### ** Examples
> 
> # Data Simulation
> dat = data.frame(Y= rep(0,100),t=1:100,trans = c(rep(0,50),rep(1,50)))
> dat$Y = apply(dat,1,function(x){rnorm(1,5*rnorm(1),6*exp(rnorm(1)))})
> dat$Y = dat$Y + 15 - quantile(dat$Y,0.3) 
> dat$Y[dat$Y<=15] = 15
> 
> 
> # Estimate the MAUC statistics of the NIRS data and test on the difference. 
> MAUCtest(dat$Y,dat$t,dat$trans,TRUE,FALSE,100)
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: MAUCtest ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataInBrief.Rmd’ using knitr
Quitting from lines 938-948 (DataInBrief.Rmd) 
Error: processing vignette 'DataInBrief.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DataInBrief.Rmd’

--- re-building ‘JEMBE.Rmd’ using knitr
Quitting from lines 468-479 (JEMBE.Rmd) 
Error: processing vignette 'JEMBE.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘JEMBE.Rmd’

SUMMARY: processing the following files failed:
  ‘DataInBrief.Rmd’ ‘JEMBE.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘installing_nlmixr.Rmd’ using rmarkdown
--- finished re-building ‘installing_nlmixr.Rmd’

--- re-building ‘running_nlmixr.Rmd’ using rmarkdown
Quitting from lines 20-28 (running_nlmixr.Rmd) 
Error: processing vignette 'running_nlmixr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘running_nlmixr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Chlorella_TRC
> ### Title: Example metabolic thermal response curves
> ### Aliases: Chlorella_TRC
> ### Keywords: dataset
> 
> ### ** Examples
> 
> data("Chlorella_TRC")
> library(ggplot2)
> ggplot(Chlorella_TRC) +
+  geom_point(aes(temp, ln.rate, col = process)) +
+  facet_wrap(~ growth.temp + flux)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘nlstimedist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tdCdfPlot
> ### Title: Plot the timedist PDF or CDF
> ### Aliases: tdCdfPlot tdPdfPlot
> 
> ### ** Examples
> 
> tdTilia <- tdData(tilia, x = "Day", y = "Trees")
> model <- timedist(data = tdTilia, x = "Day", y = "propMax", r = 0.1, c = 0.5,
+                   t = 120)
> tdCdfPlot(model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nlstimedist.Rmd’ using rmarkdown
Quitting from lines 149-150 (nlstimedist.Rmd) 
Error: processing vignette 'nlstimedist.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nlstimedist.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_nltt_values
> ### Title: Collects the nLTT values of all phylogenies in the
> ###   melted/uncast/long form
> ### Aliases: get_nltt_values
> 
> ### ** Examples
> 
>   library(ape)
>   library(ggplot2)
>   library(nLTT)
> 
>   # Create some random phylogenies
>   phylogeny1 <- rcoal(10)
>   phylogeny2 <- rcoal(20)
>   phylogeny3 <- rcoal(30)
>   phylogeny4 <- rcoal(40)
>   phylogeny5 <- rcoal(50)
>   phylogeny6 <- rcoal(60)
>   phylogeny7 <- rcoal(70)
>   phylogenies <- c(phylogeny1, phylogeny2, phylogeny3,
+     phylogeny4, phylogeny5, phylogeny6, phylogeny7
+   )
> 
>   # Obtain the nLTT values
>   dt <- 0.2
>   nltt_values <- get_nltt_values(phylogenies, dt = dt)
> 
>   # Check properties of nltt_values
>   testit::assert(names(nltt_values) == c("id", "t", "nltt"))
>   nltt_values_per_phylogeny <- (1 + (1 / dt))
>   n_phylogenies <- length(phylogenies)
>   testit::assert(nrow(nltt_values)
+     == nltt_values_per_phylogeny * n_phylogenies
+   )
> 
>   # Plot the phylognies, where the individual nLTT values are visible
>   qplot(t, nltt, data = nltt_values, geom = "point",
+     ylim = c(0,1),
+     main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)
+   ) + stat_summary(
+     fun.data = "mean_cl_boot", color = "red", geom = "smooth"
+   )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_nltt_values.Rmd’ using rmarkdown
Quitting from lines 60-65 (get_nltt_values.Rmd) 
Error: processing vignette 'get_nltt_values.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘get_nltt_values.Rmd’

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fwdplot
> ### Title: Forward plot(s) to monitor selected statistic(s)/method(s)
> ### Aliases: fwdplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(smokingcessation, package = "netmeta")
> smokingcessation$id <- 1:nrow(smokingcessation)
> 
> study912 <- subset(smokingcessation, id %in% 9:12)
> p1 <- netmeta::pairwise(list(treat1, treat2, treat3),
+                         list(event1, event2, event3),
+                         list(n1, n2, n3),
+                         data = study912,
+                         sm = "OR")
> 
> # Forward search algorithm
> #
> FSresult <- NMAoutlier(p1, P = 1, small.values = "bad", n_cores = 2)
> 
> # forward plot for Cook's distance
> fwdplot(FSresult, "cook")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown
Quitting from lines 123-150 (Examples.Rmd) 
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
invalid ‘type’ (list) of argument
--- failed re-building ‘Examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NMF-package
> ### Title: Algorithms and framework for Nonnegative Matrix Factorization
> ###   (NMF).
> ### Aliases: NMF NMF-package
> ### Keywords: package
> 
> ### ** 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 <- 50; counts <- c(5, 5, 8);
> V <- syntheticNMF(n, counts)
> 
> # perform a 3-rank NMF using the default algorithm
> res <- nmf(V, 3)
> 
> basismap(res)
Error in Ops.unit(m, unit(1, "grobwidth", textGrob(coln[i <- which.max(nchar(coln))],  : 
  REAL() can only be applied to a 'numeric', not a 'integer'
Calls: basismap ... aheatmap -> heatmap_motor -> draw_colnames -> Ops.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMF-vignette.Rnw’ using knitr
Quitting from lines 894-895 (NMF-vignette.Rnw) 
Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘NMF-vignette.Rnw’

--- re-building ‘heatmaps.Rnw’ using knitr
Quitting from lines 203-206 (heatmaps.Rnw) 
Error: processing vignette 'heatmaps.Rnw' failed with diagnostics:
REAL() can only be applied to a 'numeric', not a 'integer'
--- failed re-building ‘heatmaps.Rnw’

SUMMARY: processing the following files failed:
  ‘NMF-vignette.Rnw’ ‘heatmaps.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Loading required package: testthat

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 75-89 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting_started.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nonet_plot
> ### Title: Plot the predictions or results of nonet_ensemble
> ### Aliases: nonet_plot
> 
> ### ** Examples
> 
> # nonet_plot functionality can be explained via below example
> # Setup
> library(caret)
Loading required package: lattice
Loading required package: ggplot2
> library(nonet)
> library(ggplot2)
> 
> # Load Data
> dataframe <- data.frame(banknote_authentication[600:900, ])
> dataframe$class <- as.factor(ifelse(dataframe$class >= 1, 'Yes', 'No'))
> 
> # Spliting into train and test
> index <- createDataPartition(dataframe$class, p=0.75, list=FALSE)
> trainSet <- dataframe[ index,]
> testSet <- dataframe[-index,]
> 
> # Feature selection 
>  control <- rfeControl(functions = rfFuncs,
+   method = "repeatedcv",
+   repeats = 2,
+   verbose = FALSE)
> 
> outcomeName <- 'class'
> predictors <- c("curtosis", "entropy")
> 
> # Model Training & predictions
> banknote_rf <- train(trainSet[,predictors],trainSet[,outcomeName],method='rf')
note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

> predictions_rf_raw <- predict.train(object=banknote_rf,testSet[,predictors],type="raw")
> 
> # Results
> nonet_eval_rf <- confusionMatrix(predictions_rf_raw,testSet[,outcomeName])
> eval_rf_df <- data.frame(nonet_eval_rf$table)
> nonet_plot(eval_rf_df$Prediction, eval_rf_df$Reference, eval_rf_df, plot_type = "point")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nonet_ensemble_class.Rmd’ using rmarkdown
Quitting from lines 133-135 (nonet_ensemble_class.Rmd) 
Error: processing vignette 'nonet_ensemble_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_class.Rmd’

--- re-building ‘nonet_ensemble_clustering.Rmd’ using rmarkdown
Quitting from lines 221-222 (nonet_ensemble_clustering.Rmd) 
Error: processing vignette 'nonet_ensemble_clustering.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_clustering.Rmd’

--- re-building ‘nonet_ensemble_reg.Rmd’ using rmarkdown
Quitting from lines 128-130 (nonet_ensemble_reg.Rmd) 
Error: processing vignette 'nonet_ensemble_reg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_reg.Rmd’

SUMMARY: processing the following files failed:
  ‘nonet_ensemble_class.Rmd’ ‘nonet_ensemble_clustering.Rmd’
  ‘nonet_ensemble_reg.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘nonmem2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basic.GOF4
> ### Title: Basic 4- and 6-panel GOF
> ### Aliases: basic.GOF4 basic.GOF6
> 
> ### ** Examples
> 
> # Get path to the example files included in nonmem2R package
> file1 <- system.file("extdata", "sdtab999", package = "nonmem2R")
> sdtab<-read.table(file=file1,skip=1,header=TRUE)
> set.script.name("MyScript.R")
> ## Example 4 panel basic GOF
> basic.GOF4(subset(sdtab,DV>0),idv2="TAPD")
Error in pSummary(..., op = "max") : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: basic.GOF4 ... gtable_cbind -> Reduce -> f -> cbind_2 -> unit.pmax -> pSummary
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GOFvignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: gridExtra
Quitting from lines 28-30 (GOFvignette.Rmd) 
Error: processing vignette 'GOFvignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GOFvignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_nord
> ### Title: nord color scale for ggplot2
> ### Aliases: scale_color_nord scale_colour_nord
> 
> ### ** Examples
> 
> library(ggplot2)
> library(nord)
> 
> ggplot(diamonds) +
+  geom_point(aes(x = carat, y = price, color = cut)) +
+  scale_color_nord("lumina")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘NORRRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TASplot
> ### Title: TASplot
> ### Aliases: TASplot
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(Andes)
> TASplot(Andes, color="blue")
Warning: Removed 1 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘nparACT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nparACT-package
> ### Title: Non-Parametric Measures of Actigraphy Data
> ### Aliases: nparACT-package nparACT
> ### Keywords: package
> 
> ### ** Examples
> 
> # example function nparACT_base
> data(sleepstudy)
> r <- nparACT_base("sleepstudy", SR = 4/60) 
Warning: Removed 24 rows containing missing values (geom_bar).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: nparACT_base ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘NPflow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DPMGibbsN
> ### Title: Slice Sampling of the Dirichlet Process Mixture Model with a
> ###   prior on alpha
> ### Aliases: DPMGibbsN
> 
> ### ** Examples
> 
> rm(list=ls())
> #Number of data
> n <- 500
> #n <- 2000
> set.seed(1234)
> #set.seed(123)
> #set.seed(4321)
> 
> # Sample data
> m <- matrix(nrow=2, ncol=4, c(-1, 1, 1.5, 2, 2, -2, -1.5, -2))
> p <- c(0.2, 0.1, 0.4, 0.3) # frequence des clusters
> 
> sdev <- array(dim=c(2,2,4))
> sdev[, ,1] <- matrix(nrow=2, ncol=2, c(0.3, 0, 0, 0.3))
> sdev[, ,2] <- matrix(nrow=2, ncol=2, c(0.1, 0, 0, 0.3))
> sdev[, ,3] <- matrix(nrow=2, ncol=2, c(0.3, 0.15, 0.15, 0.3))
> sdev[, ,4] <- .3*diag(2)
> c <- rep(0,n)
> z <- matrix(0, nrow=2, ncol=n)
> for(k in 1:n){
+  c[k] = which(rmultinom(n=1, size=1, prob=p)!=0)
+  z[,k] <- m[, c[k]] + sdev[, , c[k]]%*%matrix(rnorm(2, mean = 0, sd = 1), nrow=2, ncol=1)
+  #cat(k, "/", n, " observations simulated\n", sep="")
+ }
> 
>  d<-2
>  # Set parameters of G0
>  hyperG0 <- list()
>  hyperG0[["mu"]] <- rep(0,d)
>  hyperG0[["kappa"]] <- 0.001
>  hyperG0[["nu"]] <- d+2
>  hyperG0[["lambda"]] <- diag(d)/10
> 
>  # hyperprior on the Scale parameter of DPM
>  a <- 0.0001
>  b <- 0.0001
> 
>  # Number of iterations
>  N <- 30
> 
>  # do some plots
>  doPlot <- TRUE
>  nbclust_init <- 30
> 
> 
> 
>  ## Data
>  ########
>  library(ggplot2)
>  p <- (ggplot(data.frame("X"=z[1,], "Y"=z[2,]), aes(x=X, y=Y))
+        + geom_point()
+        + ggtitle("Toy example Data"))
>  p
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘npregfast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.frfast
> ### Title: Visualization of 'frfast' objects with ggplot2 graphics
> ### Aliases: autoplot.frfast
> 
> ### ** Examples
> 
> 
> library(npregfast)
> library(ggplot2)
> 
> 
> data(barnacle)
> 
> # Nonparametric regression without interactions
> fit <- frfast(DW ~ RC, data = barnacle, nboot = 50) 
> autoplot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘nprobust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nprobust.plot
> ### Title: Graphical Presentation of Results from 'nprobust' Package.
> ### Aliases: nprobust.plot
> 
> ### ** Examples
> 
> x   <- runif(500) 
> y   <- sin(4*x) + rnorm(500)
> est <- lprobust(y,x)
> nprobust.plot(est)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘nullabor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lineup
> ### Title: The line-up protocol.
> ### Aliases: lineup
> 
> ### ** Examples
> 
> library(ggplot2)
> ggplot(lineup(null_permute('mpg'), mtcars), aes(mpg, wt)) +
+   geom_point() +
+   facet_wrap(~ .sample)
decrypt("IED2 mava ct yencvcet AA")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘distances.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 114-116 (distances.Rmd) 
Error: processing vignette 'distances.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘distances.Rmd’

--- re-building ‘nullabor-examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Removed 20 rows containing missing values (geom_rect).
Quitting from lines 78-95 (nullabor-examples.Rmd) 
Error: processing vignette 'nullabor-examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nullabor-examples.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-49 (nullabor.Rmd) 
Error: processing vignette 'nullabor.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nullabor.Rmd’

SUMMARY: processing the following files failed:
  ‘distances.Rmd’ ‘nullabor-examples.Rmd’ ‘nullabor.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NutrienTrackeR.Rmd’ using rmarkdown
Quitting from lines 146-147 (NutrienTrackeR.Rmd) 
Error: processing vignette 'NutrienTrackeR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘NutrienTrackeR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parties_v
> ### Title: New Zealand political party colours
> ### Aliases: parties_v
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Example use of parties_v in a colour scale for ggplot2
> if(require(ggplot2) & require(scales) & require(dplyr) & require(forcats)){
+ polls %>%
+     filter(MidDate > as.Date("2014-11-20") & !is.na(VotingIntention)) %>%
+     filter(Party %in% c("National", "Labour", "Green", "NZ First")) %>%
+     mutate(Party = fct_reorder(Party, VotingIntention, .desc = TRUE),
+            Party = fct_drop(Party)) %>%
+     ggplot(aes(x = MidDate, y = VotingIntention, colour = Party, linetype = Pollster)) +
+     geom_line(alpha = 0.5) +
+     geom_point(aes(shape = Pollster)) +
+     geom_smooth(aes(group = Party), se = FALSE, colour = "grey15", span = .4) +
+     scale_colour_manual(values = parties_v) +
+     scale_y_continuous("Voting intention", label = percent) +
+     scale_x_date("") +
+     facet_wrap(~Party, scales = "free_y") 
+     }
Loading required package: ggplot2
Loading required package: scales
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: forcats
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
Quitting from lines 64-82 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘README.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterDepth
> ### Title: Filter price level volume.
> ### Aliases: filterDepth
> 
> ### ** Examples
> 
> 
> # obtain price level volume for a 15 minute window.
> filtered <- with(lob.data, filterDepth(depth,
+     from=as.POSIXct("2015-05-01 02:45:00.000", tz="UTC"),
+     to=as.POSIXct("2015-05-01 03:00:00.000", tz="UTC")))
> 
> # top 5 most active price levels during this 15 minute window.
> head(sort(tapply(filtered$volume, filtered$price, length),
+     decreasing=TRUE), 5)
212.35 254.57 233.78 233.77 235.58 
    96     74     64     59     58 
> 
> # extract available volume for price level 233.78, then plot it.
> level.233.78 <- filtered[filtered$price == 233.78, c("timestamp", "volume")]
> plotTimeSeries(level.233.78$timestamp, level.233.78$volume*10^-8)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘guide.Rmd’ using rmarkdown
Quitting from lines 375-382 (guide.Rmd) 
Error: processing vignette 'guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/odbc.Rcheck/00install.out’ for details.
Running examples in ‘oddsratio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: insert_or
> ### Title: Insert odds ratios of GAM(M)s into smoothing function
> ### Aliases: insert_or
> 
> ### ** Examples
> 
> # load data (Source: ?mgcv::gam) and fit model
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
> fit_gam <- gam(y ~ s(x0) + s(I(x1^2)) + s(x2) +
+                offset(x3) + x4, data = data_gam) # fit model
> 
> # create input objects (plot + odds ratios)
> library(oddsratio)
> plot_object <- plot_gam(fit_gam, pred = "x2", title = "Predictor 'x2'")
> or_object1 <- or_gam(data = data_gam, model = fit_gam,
+                      pred = "x2", values = c(0.099, 0.198))
> 
> # insert first odds ratios to plot
> plot_object <- insert_or(plot_object, or_object1, or_yloc = 3,
+                          values_xloc = 0.04, line_size = 0.5,
+                          line_type = "dotdash", text_size = 6,
+                          values_yloc = 0.5, arrow_col = "red")
> 
> # calculate second odds ratio
> or_object2 <- or_gam(data = data_gam, model = fit_gam, pred = "x2",
+                      values = c(0.4, 0.6))
> 
> # add or_object2 into plot
> insert_or(plot_object, or_object2, or_yloc = 2.1, values_yloc = 2,
+           line_col = "green4", text_col = "black",
+           rect_col = "green4", rect_alpha = 0.2,
+           line_alpha = 1, line_type = "dashed",
+           arrow_xloc_r = 0.01, arrow_xloc_l = -0.01,
+           arrow_length = 0.01, rect = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘function_tutorial.Rmd’ using rmarkdown
Quitting from lines 88-89 (function_tutorial.Rmd) 
Error: processing vignette 'function_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘function_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OECD.Rmd’ using rmarkdown
Quitting from lines 123-131 (OECD.Rmd) 
Error: processing vignette 'OECD.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘OECD.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: body_add_gg
> ### Title: add ggplot
> ### Aliases: body_add_gg
> 
> ### ** Examples
> 
> if( require("ggplot2") ){
+   doc <- read_docx()
+ 
+   gg_plot <- ggplot(data = iris ) +
+     geom_point(mapping = aes(Sepal.Length, Petal.Length))
+ 
+   if( capabilities(what = "png") )
+     doc <- body_add_gg(doc, value = gg_plot, style = "centered" )
+ 
+   print(doc, target = tempfile(fileext = ".docx") )
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: body_add_gg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(officer)
  +   library(magrittr)
  +   library(xml2)
  + })
  > 
  > test_check("officer")
  ── 1. Error: ggplot add (@test-docx-add.R#146)  ────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: read_docx() %>% body_add_gg(value = gg_plot, style = "centered") at testthat/test-docx-add.R:146
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: withVisible(function_list[[k]](value))
  8: function_list[[k]](value)
  9: body_add_gg(., value = gg_plot, style = "centered")
  10: print(value)
  ...
  16: preDraw(x)
  17: preDraw.gTree(x)
  18: pushvpgp(x)
  19: pushgrobvp(x$vp)
  20: pushgrobvp.viewport(x$vp)
  21: pushViewport(vp, recording = FALSE)
  22: lapply(vps, push.vp, recording)
  23: FUN(X[[i]], ...)
  24: push.vp.viewport(X[[i]], ...)
  25: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 460 SKIPPED: 1 FAILED: 1
  1. Error: ggplot add (@test-docx-add.R#146) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘officer_reader.Rmd’ using rmarkdown
--- finished re-building ‘officer_reader.Rmd’

--- re-building ‘powerpoint.Rmd’ using rmarkdown
Note: zip::zip() is deprecated, please use zip::zipr() instead
Loading required package: ggplot2
Quitting from lines 235-287 (powerpoint.Rmd) 
Error: processing vignette 'powerpoint.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘powerpoint.Rmd’

--- re-building ‘word.Rmd’ using rmarkdown
Quitting from lines 146-163 (word.Rmd) 
Error: processing vignette 'word.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘word.Rmd’

SUMMARY: processing the following files failed:
  ‘powerpoint.Rmd’ ‘word.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ols_plot_added_variable
> ### Title: Added variable plots
> ### Aliases: ols_plot_added_variable ols_avplots
> 
> ### ** Examples
> 
> model <- lm(mpg ~ disp + hp + wt, data = mtcars)
> ols_plot_added_variable(model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OmicsPLS_vignette.Rmd’ using rmarkdown
Quitting from lines 87-89 (OmicsPLS_vignette.Rmd) 
Error: processing vignette 'OmicsPLS_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘OmicsPLS_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCA_plot
> ### Title: Create a PCA plot
> ### Aliases: PCA_plot
> 
> ### ** Examples
> 
> PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
+ variable = "Treatment", color = "Treatment", response_variable = "Metabolite")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Omu_vignette.Rmd’ using rmarkdown
Warning: Column `KEGG` joining factors with different levels, coercing to character vector
Warning: Column `KEGG` joining factors with different levels, coercing to character vector
Warning: Column `Metabolite` joining factors with different levels, coercing to character vector
Warning: Column `Rxn` joining factor and character vector, coercing into character vector
Warning: Column `Org` joining character vector and factor, coercing into character vector
Quitting from lines 264-267 (Omu_vignette.Rmd) 
Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Omu_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gplot
> ### Title: Box-and-Whisker Plots and Error Bars
> ### Aliases: gplot
> ### Keywords: functions
> 
> ### ** Examples
> 
> 
> library(onewaytests)
> 
> gplot(Sepal.Length ~ Species, data = iris, type = "boxplot")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘openair-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calendarPlot
> ### Title: Plot time series values in convential calendar format
> ### Aliases: calendarPlot
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> 
> # load example data from package
> data(mydata)
> 
> # basic plot
> calendarPlot(mydata, pollutant = "o3", year = 2003)
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: calendarPlot ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘osem-history.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date


Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 57-66 (osem-history.Rmd) 
Error: processing vignette 'osem-history.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘osem-history.Rmd’

--- re-building ‘osem-intro.Rmd’ using rmarkdown
Loading required package: maps
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.4-2, (SVN revision 581)
 GEOS runtime version: 3.7.1-CAPI-1.11.1 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

--- finished re-building ‘osem-intro.Rmd’

--- re-building ‘osem-serialization.Rmd’ using rmarkdown
--- finished re-building ‘osem-serialization.Rmd’

SUMMARY: processing the following file failed:
  ‘osem-history.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 141-144 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: giniChart
> ### Title: Produce a ROC curve with gini coefficient title
> ### Aliases: giniChart
> ### Keywords: AUROC gini roc
> 
> ### ** Examples
> 
>   sampledata<- data.frame(val= rnorm(100) , outcome=rbinom(100,1,.8))
>   giniChart(sampledata$val,sampledata$outcome)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘presentation.Rmd’ using rmarkdown
Quitting from lines 39-49 (presentation.Rmd) 
Error: processing vignette 'presentation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘presentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ocs-vignette.Rmd’ using rmarkdown
--- finished re-building ‘ocs-vignette.Rmd’

--- re-building ‘ped-vignette.Rmd’ using rmarkdown
Warning in kinship2::pedigree(id = Pedig$Indiv, dadid = Pedig$Sire, momid = Pedig$Dam,  :
  More than 25% of the gender values are 'unknown'
Quitting from lines 119-122 (ped-vignette.Rmd) 
Error: processing vignette 'ped-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ped-vignette.Rmd’

--- re-building ‘seg-vignette.Rmd’ using rmarkdown
--- finished re-building ‘seg-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.optweight
> ### Title: Plot Dual Variables for Assessing Balance Constraints
> ### Aliases: plot.optweight plot.optweight.svy
> 
> ### ** Examples
> 
> library("cobalt")
> data("lalonde", package = "cobalt")
> 
> #Balancing covariates between treatment groups (binary)
> ow1 <- optweight(treat ~ age + educ + married +
+                 nodegree + re74, data = lalonde,
+                 tols = c(.1, .1, .1, .1, .1),
+                 estimand = "ATT")
> 
> summary(ow1) # Note the coefficient of variation
Summary of weights:

- Weight ranges:
        Min                                  Max
treated   1                   ||          1.0000
control   0 |---------------------------| 1.5946

- Units with 5 greatest weights by group:
                                           
              2      3      4      5      6
 treated      1      1      1      1      1
            604    599    589    572    569
 control 1.5946 1.5946 1.5946 1.5946 1.5946

        Coef of Var Mean Abs Dev
treated      0.0000       0.0000
control      0.5319       0.4619
overall      0.4446       0.3227

- Effective Sample Sizes:
           Control Treated
Unweighted 429.000     185
Weighted   334.408     185
>              # and effective sample size (ESS)
> 
> plot(ow1) # age has a low value, married is high
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Running examples in ‘orderedLasso-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: orderedLasso.path
> ### Title: Fit a path of ordered lasso models
> ### Aliases: orderedLasso.path
> 
> ### ** Examples
> 
> set.seed(3)
> n = 50
> b = c(4,3,1,0)
> p = length(b)
> x = matrix(rnorm(n*p),nrow = n)
> sigma = 5
> y = x %*% b + sigma * rnorm(n, 0, 1)
> path1 = orderedLasso.path(x,y, intercept =  FALSE, 
+         method = "Solve.QP", strongly.ordered = TRUE)
> plot(path1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ordinalClust.Rmd’ using rmarkdown

Attaching package: 'ordinalClust'

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

    plot

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 14 rows containing missing values (geom_bar).
Quitting from lines 63-82 (ordinalClust.Rmd) 
Error: processing vignette 'ordinalClust.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ordinalClust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [29s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Failure: CV MSE matches previous value (@test-overall.R#36)  ─────────────
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘osmplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_axes
> ### Title: add_axes
> ### Aliases: add_axes
> 
> ### ** Examples
> 
> bbox <- get_bbox (c (-0.13, 51.5, -0.11, 51.52))
> map <- osm_basemap (bbox = bbox, bg = "gray20")
> map <- add_osm_objects (map, london$dat_BNR, col = "gray40") 
> map <- add_axes (map)
> print (map)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-maps.Rmd’ using rmarkdown
Loading osmplotr
Data (c) OpenStreetMap contributors, ODbL 1.0. http://www.openstreetmap.org/copyright
Quitting from lines 66-68 (basic-maps.Rmd) 
Error: processing vignette 'basic-maps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘basic-maps.Rmd’

--- re-building ‘data-maps.Rmd’ using rmarkdown
Loading osmplotr
Data (c) OpenStreetMap contributors, ODbL 1.0. http://www.openstreetmap.org/copyright
Quitting from lines 78-95 (data-maps.Rmd) 
Error: processing vignette 'data-maps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘data-maps.Rmd’

--- re-building ‘maps-with-ocean.Rmd’ using rmarkdown
--- finished re-building ‘maps-with-ocean.Rmd’

SUMMARY: processing the following files failed:
  ‘basic-maps.Rmd’ ‘data-maps.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotBarplot
> ### Title: Creates a bar plot for a discrete (or binary) variable
> ### Aliases: PlotBarplot
> 
> ### ** Examples
> 
> data(bankData)
> bankData = PrepData(bankData, dateNm = "date", dateGp = "months", 
+                     dateGpBp = "quarters", weightNm = NULL)
The following variables will be plotted:
Numerical: age balance duration campaign pdays previous
Categorical: job marital education default housing loan contact poutcome y

> PlotBarplot(bankData, "job")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘outbreaker2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: custom_likelihoods
> ### Title: Customise likelihood functions for outbreaker
> ### Aliases: custom_likelihoods print.custom_likelihoods
> 
> ### ** Examples
> 
> 
> ## specify a null model by disabling all likelihood components
> f_null <- function(data, param) {
+   return(0.0)
+ }
> 
> null_model <- custom_likelihoods(genetic = f_null,
+                                 timing_sampling = f_null,
+                                 timing_infections = f_null,
+                                 reporting = f_null,
+                                 contact = f_null)
> 
> null_config <- list(find_import = FALSE,
+                     n_iter = 200,
+                     sample_every = 1)
> 
> ## load data
> x <- fake_outbreak
> data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)
> 
> res_null <- outbreaker(data = data,
+                        config = null_config,
+                        likelihoods = null_model)
> 
> ## visualise ancestries to see if all transmission trees have been explored
> plot(res_null, type = "alpha")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Quitting from lines 136-143 (customisation.Rmd) 
Error: processing vignette 'customisation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 143-146 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nipah_malaysia
> ### Title: Nipah in Malaysia and Sinagapore, 1997-1999
> ### Aliases: nipah_malaysia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## show first few weeks of Dengue incidence
> head(nipah_malaysia)
        date perak negeri_sembilan selangor singapore
1 1997-01-04     0               0        0         0
2 1997-01-11     1               0        0         0
3 1997-01-18     0               0        0         0
4 1997-01-25     1               0        0         0
5 1997-02-01     1               0        0         0
6 1997-02-08     0               0        0         0
> 
> ## convert data to incidence object and plot epicurve using the incidence package
> library(incidence)
> cases <- subset(nipah_malaysia, select = c("perak", "negeri_sembilan", "selangor",
+  "singapore"))
> i <- as.incidence(cases, dates = nipah_malaysia$date, interval = 7L)
> plot(i)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-outcomerate.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 162-176 (intro-to-outcomerate.Rmd) 
Error: processing vignette 'intro-to-outcomerate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-to-outcomerate.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UnivariateOutlierDetection
> ### Title: Univariate Outlier Detection(Intersection of all the methods)
> ### Aliases: UnivariateOutlierDetection
> 
> ### ** Examples
> 
> #Create dataset
> X=iris[,1:4]
> #Outlier detection
> depthout(X,cutoff=0.05)
$`Outlier Observations`
    Sepal.Length Sepal.Width Petal.Length Petal.Width
14           4.3         3.0          1.1         0.1
23           4.6         3.6          1.0         0.2
38           4.9         3.6          1.4         0.1
42           4.5         2.3          1.3         0.3
110          7.2         3.6          6.1         2.5
118          7.7         3.8          6.7         2.2
119          7.7         2.6          6.9         2.3
132          7.9         3.8          6.4         2.0

$`Location of Outlier`
[1]  14  23  38  42 110 118 119 132

$`Outlier Probability`
[1] 0.71 0.82 0.54 0.92 1.00 1.00 1.00 0.98

> UnivariateOutlierDetection(iris[,1],cutoff=.95,Method="euclidean",rnames=FALSE)
$`Outlier Observations`
[1] 7.6 7.7 7.7 7.7 7.4 7.9 7.7

$`Location of Outlier`
[1] 106 118 119 123 131 132 136

$`Scatter plot`
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘OutliersO3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: O3plotColours
> ### Title: Set colours for O3 plots
> ### Aliases: O3plotColours
> 
> ### ** Examples
> 
> c1 <- O3prep(stackloss, k1=2, method=c("HDo", "BAC"), tolHDo=0.025, tolBAC=0.01)
> c2 <- O3plotM(c1)
> c2$gO3
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingO3plots.Rmd’ using rmarkdown
Quitting from lines 25-32 (DrawingO3plots.Rmd) 
Error: processing vignette 'DrawingO3plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DrawingO3plots.Rmd’

--- re-building ‘MultTolLevels.Rmd’ using rmarkdown
Quitting from lines 24-35 (MultTolLevels.Rmd) 
Error: processing vignette 'MultTolLevels.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MultTolLevels.Rmd’

--- re-building ‘PCPsO3.Rmd’ using rmarkdown
Quitting from lines 30-53 (PCPsO3.Rmd) 
Error: processing vignette 'PCPsO3.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PCPsO3.Rmd’

--- re-building ‘xtraO3methods.Rmd’ using rmarkdown
--- finished re-building ‘xtraO3methods.Rmd’

SUMMARY: processing the following files failed:
  ‘DrawingO3plots.Rmd’ ‘MultTolLevels.Rmd’ ‘PCPsO3.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: final.plot
> ### Title: Final plot
> ### Aliases: final.plot
> ### Keywords: utility
> 
> ### ** Examples
> 
> set.seed(20150605)
> x <- list(X1=rnorm(100),X2=rt(50,8),X3=rchisq(80,2))
> out <- overlap(x)
> final.plot(x,out$OV)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘P2C2M_Vignette.Rnw’ using Sweave
Loading required package: P2C2M
Loading required package: ggplot2
Loading required package: grid
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Error: processing vignette 'P2C2M_Vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘P2C2M_Vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘P2C2M_Vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 98-112 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Quitting from lines 70-80 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘progressive_packing.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: center_interval
> ### Title: Shift to the middle of each interval
> ### Aliases: center_interval
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(ggplot2)
> plot_set <- emergency %>%
+   thicken("hour", "h") %>%
+   count(h) %>%
+   head(24)
> 
> ggplot(plot_set, aes(h, n)) + geom_col()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  ── 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  ── 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘padr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

pad applied on the interval: day
Quitting from lines 27-36 (padr.Rmd) 
Error: processing vignette 'padr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘padr.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

pad applied on the interval: 3 hour
Quitting from lines 19-41 (padr_custom.Rmd) 
Error: processing vignette 'padr_custom.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘padr_custom.Rmd’

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

SUMMARY: processing the following files failed:
  ‘padr.Rmd’ ‘padr_custom.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pagenum_examples.Rmd’ using rmarkdown
Quitting from lines 74-79 (pagenum_examples.Rmd) 
Error: processing vignette 'pagenum_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pagenum_examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Anorexia
> ### Title: Anorexia data from Pruzek & Helmreich (2009)
> ### Aliases: Anorexia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Anorexia)
> 
> # Visualization of the cluster
> with(Anorexia,plot(paired(Prior,Post),type="profile"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘paletteer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2-scales-continuous
> ### Title: Continuous scales to use for ggplot2
> ### Aliases: ggplot2-scales-continuous scale_colour_paletteer_c
> ###   scale_color_paletteer_c scale_fill_paletteer_c
> 
> ### ** Examples
> 
> 
> if (require('ggplot2')) {
+ 
+   ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, colour = Petal.Length)) +
+     geom_point() +
+     scale_colour_paletteer_c(package = "scico", palette = "tokyo")
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘palettetown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
> qplot(Sepal.Length, Sepal.Width, colour = Species, data=iris) +
+  scale_colour_poke(pokemon = 'Metapod')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bivariate_choropleths.Rmd’ using rmarkdown
--- finished re-building ‘bivariate_choropleths.Rmd’

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

--- re-building ‘pals_examples.Rmd’ using rmarkdown
Quitting from lines 314-320 (pals_examples.Rmd) 
Error: processing vignette 'pals_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pals_examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_hazard
> ### Title: (Cumulative) (Step-) Hazard Plots.
> ### Aliases: geom_hazard GeomHazard geom_stephazard GeomStepHazard
> ###   geom_surv GeomSurv
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> library(pammtools)
> ped <- tumor[10:50,] %>% as_ped(Surv(days, status)~1)
> pam <- mgcv::gam(ped_status ~ s(tend), data=ped, family = poisson(), offset = offset)
> ndf <- make_newdata(ped, tend = unique(tend)) %>% add_hazard(pam)
> # piece-wise constant hazards
> ggplot(ndf, aes(x = tend, y = hazard)) +
+  geom_vline(xintercept = c(0, ndf$tend[c(1, (nrow(ndf)-2):nrow(ndf))]), lty = 3) +
+  geom_hline(yintercept = c(ndf$hazard[1:3], ndf$hazard[nrow(ndf)]), lty = 3) +
+  geom_stephazard() +
+  geom_step(col=2) +
+  geom_step(col=2, lty = 2, direction="vh")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘panelvar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stability
> ### Title: Stability of PVAR(p) model
> ### Aliases: stability stability.pvargmm stability.pvarfeols
> 
> ### ** Examples
> 
> data("ex1_dahlberg_data")
> stability_info <- stability(ex1_dahlberg_data)
> print(stability_info)
Eigenvalue stability condition:

             Eigenvalue    Modulus
1 0.5370657+0.00000000i 0.53706574
2 0.0633651+0.06442426i 0.09036383
3 0.0633651-0.06442426i 0.09036383

All the eigenvalues lie inside the unit circle.
PVAR satisfies stability condition.
> plot(stability_info)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘panelView-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: panelView
> ### Title: Panel Data Visualizations
> ### Aliases: panelView
> 
> ### ** Examples
> 
> library(panelView)
> data(panelView)
> panelView(turnout ~ policy_edr + policy_mail_in + policy_motor, 
+           data = turnout, index = c("abb","year"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: panelView
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parallelDist.Rnw’ using Sweave
Loading required package: ggplot2

Error: processing vignette 'parallelDist.Rnw' failed with diagnostics:
 chunk 2 (label = performanceDtw) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘parallelDist.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Parallel_Tree
> ### Title: Parallel_Tree
> ### Aliases: Parallel_Tree
> 
> ### ** Examples
> 
> #the msleep data can be found in the ggplot2 package
> #This plots the sleep totals for a number of different mammals, as well as the grand,
> # order and genus mean levels of sleep.
> Means_sleep<-Group_function(msleep,"sleep_total",c("order","genus"))
Warning in mean.default(data[, name_x[j]]) :
  argument is not numeric or logical: returning NA
> Parallel_Tree(Means_sleep)
Warning: Removed 83 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Simulating-Power.Rmd’ using rmarkdown
This is lavaan 0.6-3
lavaan is BETA software! Please report any bugs.

Attaching package: 'dplyr'

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

    collapse

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 116-126 (Simulating-Power.Rmd) 
Error: processing vignette 'Simulating-Power.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Simulating-Power.Rmd’

SUMMARY: processing the following file failed:
  ‘Simulating-Power.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pa.Rnw’ using Sweave
Loading required package: grid

Error: processing vignette 'pa.Rnw' failed with diagnostics:
 chunk 6 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘pa.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_cumhaz
> ### Title: Plotting parametric cumulative hazard curves
> ### Aliases: plot_cumhaz
> 
> ### ** Examples
> 
> data("rearrest")
> plot_cumhaz(rearrest, "lnorm", time = "months")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_cumhaz ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parmsurvfit_vig.Rmd’ using rmarkdown
Quitting from lines 55-60 (parmsurvfit_vig.Rmd) 
Error: processing vignette 'parmsurvfit_vig.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘parmsurvfit_vig.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 97-113 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: partialAR-package
> ### Title: Partial autoregression
> ### Aliases: partialAR-package partialAR
> ### Keywords: package
> 
> ### ** Examples
> 
> 
>     set.seed(1)
>     x <- rpar(1000, 0.8, 1, 0.5)  # Generate a random PAR sequence
>     fit.par(x)                  # Estimate its parameters
Fitted model:
  X[t] = M[t] + R[t]
  M[t] = 0.7314 M[t-1] + eps_M,t,  eps_M,t ~ N(0, 1.0211^2)
        (0.0571)                                 (0.0585)
  R[t] = R[t-1] + eps_R,t,         eps_R,t ~ N(0, 0.6206^2)
                                                 (0.0896)
  M_0 = 0.0000, R_0 = -0.0310
           (NA)      (1.1558)
Proportion of variance attributable to mean reversion (pvmr) = 0.7577
Negative log likelihood = 1596.99
>     plot(fit.par(x))            # Plot the estimate
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘constparty.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: RWeka
Loading required namespace: XML
Loading required package: XML
--- finished re-building ‘constparty.Rnw’

--- re-building ‘ctree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: coin
Loading required package: survival
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: Formula

Error: processing vignette 'ctree.Rnw' failed with diagnostics:
 chunk 11 (label = party-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘ctree.Rnw’

--- re-building ‘mob.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'mob.Rnw' failed with diagnostics:
 chunk 8 (label = PimaIndiansDiabetes-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'mob.Rnw'

--- re-building ‘partykit.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'partykit.Rnw' failed with diagnostics:
 chunk 3 (label = weather-plot0) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘partykit.Rnw’

SUMMARY: processing the following files failed:
  ‘ctree.Rnw’ ‘mob.Rnw’ ‘partykit.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Conditional Inference Trees
> ### Title: Conditional Inference Trees
> ### Aliases: ctree conditionalTree
> ### Keywords: tree
> 
> ### ** Examples
> 
> 
>     set.seed(290875)
> 
>     ### regression
>     airq <- subset(airquality, !is.na(Ozone))
>     airct <- ctree(Ozone ~ ., data = airq, 
+                    controls = ctree_control(maxsurrogate = 3))
>     airct

	 Conditional inference tree with 5 terminal nodes

Response:  Ozone 
Inputs:  Solar.R, Wind, Temp, Month, Day 
Number of observations:  116 

1) Temp <= 82; criterion = 1, statistic = 56.086
  2) Wind <= 6.9; criterion = 0.998, statistic = 12.969
    3)*  weights = 10 
  2) Wind > 6.9
    4) Temp <= 77; criterion = 0.997, statistic = 11.599
      5)*  weights = 48 
    4) Temp > 77
      6)*  weights = 21 
1) Temp > 82
  7) Wind <= 10.3; criterion = 0.997, statistic = 11.712
    8)*  weights = 30 
  7) Wind > 10.3
    9)*  weights = 7 
>     plot(airct)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MOB.Rnw’ using Sweave
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich

Error: processing vignette 'MOB.Rnw' failed with diagnostics:
 chunk 10 (label = BostonHousing-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'MOB.Rnw'

--- re-building ‘party.Rnw’ using Sweave
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
Loading required package: strucchange
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: coin
Loading required package: survival

Error: processing vignette 'party.Rnw' failed with diagnostics:
 chunk 12 (label = party-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘party.Rnw’

SUMMARY: processing the following files failed:
  ‘MOB.Rnw’ ‘party.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Heatmap
> ### Title: Heatmap
> ### Aliases: Heatmap
> 
> ### ** Examples
> 
> #Continuous METs
> Heatmap(sampledata);
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘passport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: country_format
> ### Title: Construct formatter function to format country codes as country
> ###   names
> ### Aliases: country_format
> 
> ### ** Examples
> 
> if (require(ggplot2, quietly = TRUE)) {
+     ggplot(data.frame(country = c("KOR", "MMR", "TWN", "COG"),
+                       y = 1:4),
+            aes(x = country, y = y)) +
+         geom_col() +
+         scale_x_discrete(labels = country_format(from = "iso3c"))
+ }
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘passport.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Parsed with column specification:
cols(
  Athlete = col_character(),
  Country = col_character(),
  NOC = col_character(),
  Gender = col_character(),
  Sport = col_character(),
  Discipline = col_character(),
  Event = col_character(),
  Event_gender = col_character(),
  Olympic_Record = col_character(),
  Olympic_Record_Type = col_character()
)
Quitting from lines 121-146 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘passport.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘PASWR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AGGRESSION
> ### Title: TV and Behavior
> ### Aliases: AGGRESSION
> ### Keywords: datasets
> 
> ### ** Examples
> 
> AL <- reshape(AGGRESSION, varying = c("violence", "noviolence"), 
+ v.names = "aggression", direction = "long")
> ggplot(data = AL, aes(x = factor(time), y = aggression, fill = factor(time))) + 
+ geom_boxplot() + labs(x = "") + scale_x_discrete(breaks = c(1, 2), 
+ labels = c("Violence", "No Violence")) + guides(fill = FALSE) + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pathfindr_manual_exec.Rmd’ using rmarkdown
--- finished re-building ‘pathfindr_manual_exec.Rmd’

--- re-building ‘pathfindr_vignette.Rmd’ using rmarkdown
Quitting from lines 168-185 (pathfindr_vignette.Rmd) 
Error: processing vignette 'pathfindr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pathfindr_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imagebar
> ### Title: Plot a bar chart with bars filled with png and jpeg images.
> ### Aliases: imagebar
> 
> ### ** Examples
> 
> library(patternplot)
> library(jpeg)
> 
> #http://all-free-download.com/free-vector/modern-seamless-pattern.html
> childcare<-readJPEG(system.file("img", "childcare.jpg", package="patternplot"))
> food<-readJPEG(system.file("img", "food.jpg", package="patternplot"))
> housing <-readJPEG(system.file("img", "housing.jpg", package="patternplot"))
> 
> #Example 1
> data <- read.csv(system.file("extdata", "monthlyexp.csv", package="patternplot"))
> data<-data[which(data$Location=='City 1'),]
> x<-factor(data$Type, c('Housing', 'Food',  'Childcare'))
> y<-data$Amount
> pattern.type<-list(housing, food, childcare)
> imagebar(data,x, y,group=NULL,pattern.type=pattern.type,
+          frame.color=c('darkred', 'darkgreen', 'orange'),
+          ylab='Monthly Expenses, Dollars')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘patternplot-intro.Rmd’ using docco_linear
Quitting from lines 28-47 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘patternplot-intro.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ba_plot
> ### Title: Create a Bland-Altman plot
> ### Aliases: ba_plot
> 
> ### ** Examples
> 
> data(ex_data, package = "PAutilities")
> 
> # Reduce the number of data points (for illustration purposes) by isolating
> # the 150 largest cases
> 
> illustration_threshold <-
+     quantile(ex_data$Axis1, probs = 1 - (150 / nrow(ex_data)))
> ex_data <- ex_data[ex_data$Axis1 > illustration_threshold, ]
> 
> # Generate the plot
> my_ba <- ba_plot(
+     ex_data,
+     "(Axis1 + Axis3) / 2",
+     "Axis1 - Axis3",
+     "mean(Axis1, Axis3)",
+     "Axis1 - Axis3"
+ )
> 
> my_ba
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pauwels2014.Rnw’ using Sweave
Loading required package: deSolve
Loading required package: ggplot2
Error: processing vignette 'pauwels2014.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pauwels2014.Rnw’

SUMMARY: processing the following file failed:
  ‘pauwels2014.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
> subflu = flu[flu$region=="Mazowieckie", ]
> # linear scale
> qplot(date, inception.rate,data=subflu, geom="line")+scale_y_sqrt() +theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pcadapt.Rmd’ using rmarkdown
Quitting from lines 67-68 (pcadapt.Rmd) 
Error: processing vignette 'pcadapt.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pcadapt.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CEPlot
> ### Title: Cumulative eigenvalue plot
> ### Aliases: CEPlot
> 
> ### ** Examples
> 
> #load iris data
> data(iris)
> 
> #Define grouping variable, grouping the observations by whether their species is
> #Setosa or not
> iris$group <- "setosa"
> iris$group[iris$Species != "setosa"] <- "non-setosa"
> iris$Species <- NULL
> 
> ## Not run: 
> ##D #make a PCADSC object, splitting the data by "group"
> ##D irisPCADSC <- PCADSC(iris, "group")
> ##D 
> ##D #make a partial PCADSC object from iris and fill out CEInfo in the next call
> ##D irisPCADSC2 <- PCADSC(iris, "group", doCE = FALSE)
> ##D irisPCADSC2 <- doCE(irisPCADSC2)
> ##D 
> ##D #make a CE plot
> ##D CEPlot(irisPCADSC)
> ##D CEPlot(irisPCADSC2)
> ## End(Not run)
> 
> #Only do CE information and use less resamplings for a faster runtime
> irisPCADSC_fast <- PCADSC(iris, "group", doAngle = FALSE, doChroma = FALSE,
+   B = 1000)
> CEPlot(irisPCADSC_fast)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PCMBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCMTrajectory
> ### Title: Generate a trajectory for the mean in one regime of a PCM
> ### Aliases: PCMTrajectory
> 
> ### ** Examples
> 
> set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
> 
> # a Brownian motion model with one regime
> modelOU <- PCM(model = PCMDefaultModelTypes()['F'], k = 2)
> 
> # assign the model parameters at random: this will use uniform distribution
> # with boundaries specified by PCMParamLowerLimit and PCMParamUpperLimit
> # We do this in two steps:
> # 1. First we generate a random vector. Note the length of the vector equals
> # PCMParamCount(modelBM).
> 
> randomParams <- PCMParamRandomVecParams(
+   modelOU, PCMNumTraits(modelOU), PCMNumRegimes(modelOU))
> # 2. Then we load this random vector into the model.
> PCMParamLoadOrStore(
+   modelOU,
+   randomParams,
+   0, PCMNumTraits(modelBM), PCMNumRegimes(modelBM), load = TRUE)
[1] 11
> 
> # let's plot the trajectory of the model starting from X0 = c(0,0)
> PCMTrajectory(
+   model = modelOU,
+   X0 = c(0, 0),
+   doPlot2D = TRUE)
Warning: Removed 98 rows containing non-finite values (stat_ellipse).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcr_analyze
> ### Title: Apply qPCR analysis methods
> ### Aliases: pcr_analyze
> 
> ### ** Examples
> 
> # applying the delta delta ct method
> ## locate and read raw ct data
> fl <- system.file('extdata', 'ct1.csv', package = 'pcr')
> ct1 <- readr::read_csv(fl)
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
> 
> # add grouping variable
> group_var <- rep(c('brain', 'kidney'), each = 6)
> 
> # calculate all values and errors in one step
> pcr_analyze(ct1,
+             group_var = group_var,
+             reference_gene = 'GAPDH',
+             reference_group = 'brain',
+             method = 'delta_delta_ct')
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
# A tibble: 2 x 8
  group  gene  normalized calibrated relative_expression  error lower upper
  <chr>  <chr>      <dbl>      <dbl>               <dbl>  <dbl> <dbl> <dbl>
1 brain  c_myc       6.86       0                   1    0.174  0.886  1.13
2 kidney c_myc       4.36      -2.50                5.64 0.0954 5.28   6.02
> 
> # return a plot
> pcr_analyze(ct1,
+             group_var = group_var,
+             reference_gene = 'GAPDH',
+             reference_group = 'brain',
+             method = 'delta_delta_ct',
+             plot = TRUE)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qpcr_analysis.Rmd’ using rmarkdown
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)

Attaching package: 'cowplot'

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

    ggsave

Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = "gene"
Quitting from lines 412-421 (qpcr_analysis.Rmd) 
Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qpcr_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PDQutils.Rnw’ using knitr
Quitting from lines 734-750 (PDQutils.Rnw) 
Error: processing vignette 'PDQutils.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PDQutils.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘depth_ranktests.Rmd’ using rmarkdown
--- finished re-building ‘depth_ranktests.Rmd’

--- re-building ‘wavelet_est_clust.Rmd’ using rmarkdown
Quitting from lines 257-258 (wavelet_est_clust.Rmd) 
Error: processing vignette 'wavelet_est_clust.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wavelet_est_clust.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binSum
> ### Title: binSum
> ### Aliases: binSum
> 
> ### ** Examples
> 
> ## bins of size 3bp.
> ## -1-   -3-   -5-
> ##    -2-   -4-
> ## 123456789012345 base index.
> ## --2---
> ##       --1-
> ##           --0-------
> ## Coverage profile.
> profile <- data.frame(chromStart=as.integer(c(0, 6, 10)),
+                       chromEnd=as.integer(c(6, 10, 10000)),
+                       count=as.integer(c(2, 1, 0)))
> library(PeakSegJoint)
> bins <- binSum(profile,
+                bin.chromStart=0L,
+                bin.size=3L,
+                n.bins=2000L)
> library(ggplot2)
> bases <- data.frame(position=1:15, base="N")
> ggplot()+
+   ylab("")+
+   geom_text(aes(position, 0, label=base),
+             data=bases)+
+   geom_step(aes(chromStart+0.5, count, color=what),
+             data=data.frame(profile, what="profile"),
+             size=2)+
+   geom_step(aes(chromStart+0.5, count, color=what),
+             data=data.frame(bins, what="bin total"))+
+   geom_step(aes(chromStart+0.5, mean, color=what),
+             data=data.frame(bins, what="bin mean"))+
+   coord_cartesian(xlim=c(0, max(bases$position)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PedCNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.clust
> ### Title: Plots clustering result
> ### Aliases: plot.clust
> 
> ### ** Examples
> 
> # Fit the data under the given clustering numbers
> clus.fit <- ClusProc(signal=signal,N=2:6,varSelection='PC.9')
The first 5 principal components are used.
The logliklihood for signal model is -1663.629 when clustering number is 2.
The logliklihood for signal model is -1477.954 when clustering number is 3.
The logliklihood for signal model is -1394.682 when clustering number is 4.
The logliklihood for signal model is -1342.043 when clustering number is 5.
The logliklihood for signal model is -1282.491 when clustering number is 6.
> plot(clus.fit,type='histo')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘penaltyLearning-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ROChange
> ### Title: ROC curve for changepoints
> ### Aliases: ROChange
> 
> ### ** Examples
> 
> 
> library(penaltyLearning)
> data(neuroblastomaProcessed, envir=environment())
> ## Get incorrect labels data for one profile.
> pid <- 11
> pro.errors <- neuroblastomaProcessed$errors[profile.id==pid,]
> ## Get the feature that corresponds to the BIC penalty = log(n),
> ## meaning log(penalty) = log(log(n)).
> chr.vec <- paste(c(1:4, 11, 17))
> pid.names <- paste0(pid, ".", chr.vec)
> BIC.feature <- neuroblastomaProcessed$feature.mat[pid.names, "log2.n"]
> pred <- data.table(pred.log.lambda=BIC.feature, chromosome=chr.vec)
> result <- ROChange(pro.errors, pred, "chromosome")
> library(ggplot2)
> ## Plot the ROC curves.
> ggplot()+
+   geom_path(aes(FPR, TPR), data=result$roc)+
+   geom_point(aes(FPR, TPR, color=threshold), data=result$thresholds, shape=1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘peptider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detection probability in a single library of size N
> ### Aliases: detect
> 
> ### ** Examples
> 
> summary(detect())
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.003628 0.061622 0.242643 0.360004 0.602151 0.999647 
> 
> require(ggplot2)
Loading required package: ggplot2
> lib <- libscheme("NNK", 7)
> qplot(detect(lib, size=10^8), weight=di, geom="histogram", data=lib$data)
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘perc_calculator_example.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 198-205 (perc_calculator_example.Rmd) 
Error: processing vignette 'perc_calculator_example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘perc_calculator_example.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘permutes.Rmd’ using rmarkdown
Quitting from lines 125-126 (permutes.Rmd) 
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘permutes.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check.overlap
> ### Title: Check propensity score overlap
> ### Aliases: check.overlap
> 
> ### ** Examples
> 
> library(personalized)
> 
> set.seed(123)
> n.obs  <- 250
> n.vars <- 15
> x <- matrix(rnorm(n.obs * n.vars, sd = 3), n.obs, n.vars)
> 
> 
> # simulate non-randomized treatment
> xbetat   <- 0.25 + 0.5 * x[,11] - 0.5 * x[,12]
> trt.prob <- exp(xbetat) / (1 + exp(xbetat))
> trt01    <- rbinom(n.obs, 1, prob = trt.prob)
> 
> # create function for fitting propensity score model
> prop.func <- function(x, trt)
+ {
+     # fit propensity score model
+     propens.model <- cv.glmnet(y = trt,
+                                x = x, family = "binomial")
+     pi.x <- predict(propens.model, s = "lambda.min",
+                     newx = x, type = "response")[,1]
+     pi.x
+ }
> 
> check.overlap(x = x,
+               trt = trt01,
+               propensity.func = prop.func)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage_of_the_personalized_package.Rmd’ using rmarkdown
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
Loading required package: gbm
Loaded gbm 2.1.5
Loading required package: ggplot2
Loading required package: plotly

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 176-177 (usage_of_the_personalized_package.Rmd) 
Error: processing vignette 'usage_of_the_personalized_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usage_of_the_personalized_package.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perspectev.test
> ### Title: Test for irreducibility of relationship between upper level
> ###   traits and survivorship
> ### Aliases: perspectev.test
> 
> ### ** Examples
> 
> 	data(testData)
> 
>   	data = perspectev.read(testData,extinctionAge=5,occurrenceAge="Age",
+   	upper="Genus",lower="Species",traits=c("Lat","Long"),traitfun=mcpRange,projection=FALSE)
[1] "Assigning survivorship = 1 to taxa with ages < extinctionAge (backward time)"
  traitdata_index traitdata_value
1               1             Lat
2               2            Long
> 
>   	#4 iterations chosen out of convenience - use more!
> 	mcpTest  = perspectev.test(data,4,1,traitfun=mcpRange)
> 	mcpSim  = perspectev.simulate(data,4,1,traitfun=mcpRange)
[1] "Intercept and slope parameters not specified. Assigning model fit through logistic regression."
[1] "Level parameter not specified (can be 'lower' or 'upper'). Performing upper level simulation."
[1] "Binary/continuous survivorship not specified, setting binary = TRUE"
[1] "Upper Level Selection Intercept -2.2264213772787"
[1] "Upper Level Selection Slope -0.273533830039319"
> 	perspectev.plot(mcpTest,list(mcpSim),c("S1"),"Test")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘artificial_intelligence_evolution.Rmd’ using rmarkdown
Quitting from lines 38-48 (artificial_intelligence_evolution.Rmd) 
Error: processing vignette 'artificial_intelligence_evolution.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘artificial_intelligence_evolution.Rmd’

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

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

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

Error: Vignette re-building 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-patched-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Fuzzy matching
Phonetic matching
Semantic matching
Fuzzy matching
Phonetic matching
Semantic matching
Quitting from lines 1112-1120 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: opt_FUN
> ### Title: Unified optimization function
> ### Aliases: opt_FUN opt_ucminf opt_nlminb opt_nlm opt_optim
> 
> ### ** Examples
> 
> library(phenofit)
> library(ggplot2)
> library(magrittr)
> library(purrr)

Attaching package: ‘purrr’

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

    set_names

> 
> # simulate vegetation time-series
> fFUN = doubleLog.Beck
> par = c(
+   mn  = 0.1,
+   mx  = 0.7,
+   sos = 50,
+   rsp = 0.1,
+   eos = 250,
+   rau = 0.1)
> t    <- seq(1, 365, 8)
> tout <- seq(1, 365, 1)
> y <- fFUN(par, t)
> 
> # initial parameter
> par0 <- c(
+   mn  = 0.15,
+   mx  = 0.65,
+   sos = 100,
+   rsp = 0.12,
+   eos = 200,
+   rau = 0.12)
> 
> objective <- f_goal # goal function
> optFUNs   <- c("opt_ucminf", "opt_nlminb", "opt_nlm", "opt_optim") %>% set_names(., .)
> 
> opts <- lapply(optFUNs, function(optFUN){
+     optFUN <- get(optFUN)
+     opt <- optFUN(par0, objective, y = y, t = t, fun = fFUN)
+     opt$ysim <- fFUN(opt$par, t)
+     opt
+ })
> 
> # visualization
> df   <- map(opts, "ysim") %>% as.data.frame() %>% cbind(t, y, .)
> pdat <- reshape2::melt(df, c("t", "y"), variable.name = "optFUN")
> 
> ggplot(pdat) + 
+     geom_point(data = data.frame(t, y), aes(t, y), size = 2) + 
+     geom_line(aes(t, value, color = optFUN), size = 0.9)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PhenotypeSimulator.Rmd’ using rmarkdown
--- finished re-building ‘PhenotypeSimulator.Rmd’

--- re-building ‘Sample-scripts-external-genotype-simulation.Rmd’ using rmarkdown
--- finished re-building ‘Sample-scripts-external-genotype-simulation.Rmd’

--- re-building ‘Simulation-and-LinearModel.Rmd’ using rmarkdown
Quitting from lines 196-258 (Simulation-and-LinearModel.Rmd) 
Error: processing vignette 'Simulation-and-LinearModel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Simulation-and-LinearModel.Rmd’

SUMMARY: processing the following file failed:
  ‘Simulation-and-LinearModel.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Quitting from lines 198-199 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologyInOut', please, see https://www.r4photobiology.info/
For on-line documentation see https://docs.r4photobiology.info/photobiologyInOut/

Attaching package: 'lubridate'

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

    date

Loading required package: lattice
Loading required package: grid
Package hyperSpec, version 0.99-20180627

To get started, try
   vignette ("hyperspec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org


This is colorSpec.  Version: 0.8-3.  Author: Glenn Davis [aut, cre].  Built: R 3.6.0; ; 2019-03-29
 14:16:29 UTC; unix

Attaching package: 'colorSpec'

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

    bind

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

    normalize

Read 3 items
Read 16 items
Quitting from lines 131-132 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologyLamps', please, see http://www.r4photobiology.info/
For on-line documentation see http://docs.r4photobiology.info/photobiologyLamps/
Quitting from lines 167-168 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Quitting from lines 209-210 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataplotsPlants.Rnw’ using knitr
Quitting from lines 79-81 (dataplotsPlants.Rnw) 
Error: processing vignette 'dataplotsPlants.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dataplotsPlants.Rnw’

--- re-building ‘userguideplants.Rnw’ using knitr
Warning in Red("Smith") :
  The definition of 'Smith' defaults to 'Smith10', to restore old behaviour use 'Smith20'.
Warning in Far_red("Smith") :
  The definition of 'Smith' defaults to 'Smith10', to restore old behaviour use 'Smith20'.
Quitting from lines 102-106 (userguideplants.Rnw) 
Error: processing vignette 'userguideplants.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userguideplants.Rnw’

SUMMARY: processing the following files failed:
  ‘dataplotsPlants.Rnw’ ‘userguideplants.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: photobiologySensors-package
> ### Title: photobiologySensors: Spectral Response Data for Light Sensors
> ### Aliases: photobiologySensors photobiologySensors-package
> 
> ### ** Examples
> 
> library(photobiology)
> library(photobiologyWavebands)
> library(ggspectra)
Loading required package: ggplot2
> 
> names(sensors.mspct)
 [1] "Berger_UV_Biometer" "BF5"                "flat_e"            
 [4] "flat_q"             "CUV_5"              "PQS1"              
 [7] "UVS_A"              "UVS_B"              "UVS_E"             
[10] "LI_190"             "LI_200"             "LI_210"            
[13] "TOCON_blue4"        "SG01D_A"            "SG01D_B"           
[16] "SG01D_C"            "SG01L"              "SKE510"            
[19] "SKL310"             "SKP210"             "SKP215"            
[22] "SKR110_FR"          "SKR110_R"           "SKS1110"           
[25] "SKU421"             "SKU421a"            "SKU430a"           
[28] "SKU440a"            "SL_501_high_UVA"    "SL_501_low_UVA"    
[31] "SL_501_typical"     "SM60"               "E1c"               
[34] "BW_20"             
> 
> licor_sensors
[1] "LI_190" "LI_200" "LI_210"
> par_sensors
[1] "SKP215" "SKE510" "SKP210" "PQS1"   "LI_190" "BF5"   
> intersect(par_sensors, licor_sensors)
[1] "LI_190"
> 
> photon_as_default()
> 
> response(sensors.mspct$LI_190, w.band = PAR(), quantity = "contribution.pc")
 Total PAR 
  99.18297 
attr(,"time.unit")
[1] "second"
attr(,"radiation.unit")
[1] "photon response contribution.pc"
> 
> plot(sensors.mspct$LI_190, w.band = PAR(), label.qty = "contribution.pc")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologySensors', please, see http://www.r4photobiology.info/
For on-line documentation see http://docs.r4photobiology.info/photobiologySensors/
Quitting from lines 150-151 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/

Attaching package: 'lubridate'

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

    date

Quitting from lines 86-87 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Phxnlme-package
> ### Title: Package 'Phxnlme'
> ### Aliases: Phxnlme-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(ex1phxd)
> phxd=ex1phxd
> phxplot(phxd=phxd,plot.type="residual.scatter",outpdf=FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: phxplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘phylopath-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DAG
> ### Title: Directed acyclic graphs (DAGs)
> ### Aliases: DAG
> 
> ### ** Examples
> 
>   # Use formula notation to create DAGs:
>   plot(DAG(A~B, B~C))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘binary_models.Rmd’ using rmarkdown
Quitting from lines 51-70 (binary_models.Rmd) 
Error: processing vignette 'binary_models.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘binary_models.Rmd’

--- re-building ‘intro_to_phylopath.Rmd’ using rmarkdown
Quitting from lines 114-115 (intro_to_phylopath.Rmd) 
Error: processing vignette 'intro_to_phylopath.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_to_phylopath.Rmd’

SUMMARY: processing the following files failed:
  ‘binary_models.Rmd’ ‘intro_to_phylopath.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_permutations
> ### Title: Plots the permutation distribution
> ### Aliases: plot_permutations
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech")
> plot_permutations(gt)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gt_vignette.Rmd’ using rmarkdown
Quitting from lines 175-176 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gt_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_phylota_pa
> ### Title: Plot presence/absence matrix
> ### Aliases: plot_phylota_pa
> 
> ### ** Examples
> 
> library(phylotaR)
> data(cycads)
> # drop all but first ten
> cycads <- drop_clstrs(cycads, cycads@cids[1:10])
> # plot all
> p <- plot_phylota_pa(phylota = cycads, cids = cycads@cids, txids = cycads@txids)
> print(p)  # lots of information, difficult to interpret
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Everest.Rmd’ using rmarkdown
--- finished re-building ‘Everest.Rmd’

--- re-building ‘IdealWeightComparison.Rmd’ using rmarkdown
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette 'IdealWeightComparison.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IdealWeightComparison.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required namespace: reshape2
--- finished re-building ‘NeonatalVentilation.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourPlot
> ### Title: 2-dimensional contour plot of a factorial design model
> ### Aliases: contourPlot
> 
> ### ** Examples
> 
> 
> # 2-factor example
> # ----------------
> T <- c(-1, +1, -1, +1)  # centered and scaled temperature
> S <- c(-1, -1, +1, +1)  # centered and scaled speed variable
> y <- c(69, 60, 64, 53)  # conversion, is our response variable, y
> doe.model <- lm(y ~ T + S + T * S)  # model with main effects, and interaction
> contourPlot(doe.model)  
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: contourPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pifpaf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: counterfactual.plot
> ### Title: Plot exposure's distribution under counterfactual scenario
> ### Aliases: counterfactual.plot
> 
> ### ** Examples
> 
> 
> #Example 1: Bivariate exposure
> #--------------------------------------------------------
> set.seed(2783569)
> X   <- data.frame(Exposure = 
+            sample(c("Exposed","Unexposed"), 100, replace = TRUE, 
+            prob = c(0.3, 0.7)))
> cft <- function(X){
+ 
+      #Find which indivuals are exposed
+      exposed    <- which(X[,"Exposure"] == "Exposed")
+      
+      #Change 1/3 of exposed to unexposed
+      reduced               <- sample(exposed, length(exposed)/3)
+      X[reduced,"Exposure"] <- "Unexposed"
+      
+      return(X)
+ }  
> counterfactual.plot(X, cft)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_pifpaf_package.Rmd’ using rmarkdown
Loading required package: pifpaf
Loading required package: ggplot2
Quitting from lines 133-134 (Introduction_to_pifpaf_package.Rmd) 
Error: processing vignette 'Introduction_to_pifpaf_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction_to_pifpaf_package.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cima
> ### Title: Plot Results
> ### Aliases: plot.cima
> 
> ### ** Examples
> 
> data(sbp, package = "pimeta")
> ciex <- pimeta::cima(sbp$y, sbp$sigmak, method = "DL")
> cairo_pdf("forestplot.pdf", width = 6, height = 3, family = "Arial")
> plot(ciex, digits = 2, base_size = 10, studylabel = sbp$label)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot -> plot.cima
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pimeta.Rmd’ using rmarkdown
Quitting from lines 16-29 (pimeta.Rmd) 
Error: processing vignette 'pimeta.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pimeta.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.qpin
> ### Title: PIN Visualization
> ### Aliases: ggplot.qpin
> 
> ### ** Examples
> 
> # Loading one year of simulated daily buys and sells
> 
> data('BSfrequent2015')
> 
> # Quarterly estimates for model parameters and the probability of informed trading
> # Rownames of 'BSfrequent2015' equal the business days in 2015.
> 
> qpin_list <- qpin(numbuys = BSfrequent2015[,"Buys"], numsells = BSfrequent2015[,"Sells"],
+                   dates = as.Date(rownames(BSfrequent2015), format = "%Y-%m-%d"))
> 
> # Visualization of quarterly estimates
> library(ggplot2)
> ggplot(qpin_list[["res"]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pinbasicVignette.Rmd’ using rmarkdown
pin_ll(param = NULL, numbuys = NULL, numsells = NULL,
    factorization = "Lin_Ke")
initial_vals(numbuys = NULL, numsells = NULL, method = "HAC", length = 5,
    num_clust = 5, details = FALSE)
Quitting from lines 91-93 (./Examples/Examples.Rmd) 
Quitting from lines 70-71 (./Examples/Examples.Rmd) 
Error: processing vignette 'pinbasicVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pinbasicVignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: strikeFX
> ### Title: Visualize PITCHf/x strikezones
> ### Aliases: strikeFX
> 
> ### ** Examples
> 
> data(pitches)
> 
> strikeFX(pitches)
Warning: Removed 56 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_pkggraph.Rmd’ using rmarkdown
Quitting from lines 34-58 (vignette_pkggraph.Rmd) 
Error: processing vignette 'vignette_pkggraph.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_pkggraph.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AUC-Calculation-with-PKNCA.Rmd’ using rmarkdown
Quitting from lines 22-43 (AUC-Calculation-with-PKNCA.Rmd) 
Error: processing vignette 'AUC-Calculation-with-PKNCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘AUC-Calculation-with-PKNCA.Rmd’

--- re-building ‘Data-Cleaning-in-PKNCA.Rmd’ using rmarkdown
--- finished re-building ‘Data-Cleaning-in-PKNCA.Rmd’

--- re-building ‘Introduction-and-Usage.Rmd’ using rmarkdown
--- finished re-building ‘Introduction-and-Usage.Rmd’

--- re-building ‘Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd’ using rmarkdown
--- finished re-building ‘Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd’

--- re-building ‘Options-for-Controlling-PKNCA.Rmd’ using rmarkdown
--- finished re-building ‘Options-for-Controlling-PKNCA.Rmd’

--- re-building ‘PKNCA-validation.Rmd’ using rmarkdown
--- finished re-building ‘PKNCA-validation.Rmd’

--- re-building ‘Selection-of-Calculation-Intervals.Rmd’ using rmarkdown
Quitting from lines 28-55 (Selection-of-Calculation-Intervals.Rmd) 
Error: processing vignette 'Selection-of-Calculation-Intervals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Selection-of-Calculation-Intervals.Rmd’

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

--- re-building ‘Writing-Parameter-Functions.Rmd’ using rmarkdown
--- finished re-building ‘Writing-Parameter-Functions.Rmd’

SUMMARY: processing the following files failed:
  ‘AUC-Calculation-with-PKNCA.Rmd’
  ‘Selection-of-Calculation-Intervals.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: color_pallete
> ### Title: design-quality color palletes to use in ggplot2
> ### Aliases: color_pallete
> 
> ### ** Examples
> 
> library(PKPDmisc)
> library(ggplot2)
> 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

> ggplot(sd_oral_richpk %>% filter(ID < 10), 
+ aes(x = Time,
+ y= Conc, 
+ group = ID, 
+ color = Gender)) + 
+   geom_line(size = 1.5) + scale_color_manual(values =color_pallete(1)) +
+   base_theme()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multiplot.Rmd’ using rmarkdown
Quitting from lines 28-31 (multiplot.Rmd) 
Error: processing vignette 'multiplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘multiplot.Rmd’

--- re-building ‘noncompartmental-analysis.Rmd’ using rmarkdown
--- finished re-building ‘noncompartmental-analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Network of items is not strongly connected
Removed rankings with less than 2 items
Quitting from lines 806-807 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘decay_rates.Rmd’ using knitr
--- finished re-building ‘decay_rates.Rmd’

--- re-building ‘fresnel.Rmd’ using knitr
--- finished re-building ‘fresnel.Rmd’

--- re-building ‘gaussian.rmd’ using knitr
Loading required package: dielectric
Quitting from lines 137-177 (gaussian.rmd) 
Error: processing vignette 'gaussian.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gaussian.rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DetectPlasmaMutation
> ### Title: function DetectPlasmaMutation
> ### Aliases: DetectPlasmaMutation
> 
> ### ** Examples
> 
>      patient.dir=system.file("extdata","4test_only/case/",package="PlasmaMutationDetector")
>      if (substr(patient.dir,nchar(patient.dir),nchar(patient.dir))!='/')
+        patient.dir = paste0(patient.dir,'/') # TO RUN UNDER WINDOWS
>      DetectPlasmaMutation(patient.dir,output.dir=paste0(tempdir(),'/'))
[1] "Looking for bam and bai in /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/case/rBAM/ ..."
[1] "Detecting mutations from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/case/BER/case1.chr7_MAF.txt"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DetectPlasmaMutation ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Plasmidprofiler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: main
> ### Title: Main: Run everything
> ### Aliases: main
> 
> ### ** Examples
> 
> main(blastdata,
+ srst2data,
+ coverage.filter=NA,
+ sureness.filter=0.75,
+ length.filter=10000,
+ main.title="Example Results")
Selecting by pident
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: main ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘platetools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_grid
> ### Title: Plots multiple b-scored normalised platemaps
> ### Aliases: b_grid
> 
> ### ** Examples
> 
> df01 <- data.frame(well = num_to_well(1:96),
+   vals = rnorm(96),
+   plate = 1)
> 
> df02 <- data.frame(well = num_to_well(1:96),
+   vals = rnorm(96),
+   plate = 2)
> 
> df <- rbind(df01, df02)
> 
> b_grid(data = df$vals,
+     well = df$well,
+     plate_id = df$plate,
+     plate = 96)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘plot3logit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: field3logit
> ### Title: Computation of the vector field
> ### Aliases: field3logit plot3logit print.field3logit plot.field3logit
> ###   as.data.frame.field3logit fortify.field3logit
> 
> ### ** Examples
> 
> data(cross_1year)
> 
> # Model fit
> mod0 <- nnet::multinom(employment_sit ~ finalgrade + irregularity + hsscore,
+   cross_1year)
# weights:  21 (12 variable)
initial  value 3605.645531 
iter  10 value 2187.709284
iter  20 value 2157.087955
final  value 2157.087854 
converged
> mod0
Call:
nnet::multinom(formula = employment_sit ~ finalgrade + irregularity + 
    hsscore, data = cross_1year)

Coefficients:
           (Intercept) finalgradeLow finalgradeHigh irregularityLow
Unemployed  -0.4481761    0.05551765    -0.07810893     -0.01874354
Trainee     -1.3751140    0.14456683    -0.26849829      0.05764144
           irregularityLong      hsscore
Unemployed       0.15691595 -0.016619227
Trainee         -0.03477569 -0.009964381

Residual Deviance: 4314.176 
AIC: 4338.176 
> 
> # Assessing the effect of "finalgradeHigh" (explicit notation)
> field0 <- field3logit(mod0, c(0, 0, 1, 0, 0, 0))
> gg3logit(field0) + stat_3logit()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘plotGMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_mix_comps
> ### Title: Plot a Mixture Component
> ### Aliases: plot_mix_comps
> 
> ### ** Examples
> 
> set.seed(1)
> mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
number of iterations= 29 
> x <- mixmdl$x
> x <- data.frame(x)
> ggplot2::ggplot(data.frame(x)) +
+   ggplot2::geom_histogram(ggplot2::aes(x, ..density..)) +
+   ggplot2::stat_function(geom = "line", fun = plot_mix_comps,
+                 args = list(mixmdl$mu[1], mixmdl$sigma[1], lam = mixmdl$lambda[1]),
+                 colour = "red") +
+   ggplot2::stat_function(geom = "line", fun = plot_mix_comps,
+                 args = list(mixmdl$mu[2], mixmdl$sigma[2], lam = mixmdl$lambda[2]),
+                colour = "blue")
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘plotluck-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotluck
> ### Title: "I'm feeling lucky" for ggplot
> ### Aliases: plotluck
> ### Keywords: aplot, dplot hplot,
> 
> ### ** Examples
> 
> # Single-variable density
> data(diamonds, package='ggplot2')
> plotluck(diamonds, price~1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plotluck)
  > 
  > test_check("plotluck")
  *** 1D density plot ***
  ── 1. Error: (unknown) (@test_plotluck.R#57)  ──────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: test_that_ref("1d_density", "1D density plot", {
         eq_ref(plotluck(iris, Petal.Length ~ 1))
     }) at testthat/test_plotluck.R:57
  2: eq_ref(plotluck(iris, Petal.Length ~ 1)) at testthat/test_plotluck.R:58
  3: print(x) at testthat/test_plotluck.R:39
  4: print.ggplot(x)
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_plotluck.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotluck.Rmd’ using rmarkdown
Quitting from lines 36-39 (plotluck.Rmd) 
Error: processing vignette 'plotluck.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotluck.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: highlight
> ### Title: Query graphical elements in multiple linked views
> ### Aliases: highlight
> 
> ### ** Examples
> 
> 
> # These examples are designed to show you how to highlight/brush a *single*
> # view. For examples of multiple linked views, see `demo(package = "plotly")` 
> 
> library(crosstalk)
> d <- highlight_key(txhousing, ~city)
> p <- ggplot(d, aes(date, median, group = city)) + geom_line()
> gg <- ggplotly(p, tooltip = "city") 
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggplotly ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Running examples in ‘plotMElm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_me
> ### Title: Plot marginal effects from two-way interactions in linear
> ###   regressions
> ### Aliases: plot_me
> 
> ### ** Examples
> 
> ## Continuous Term1 and Term2
> # Estimate model
> states <- as.data.frame(state.x77)
> m1 <- lm(Murder ~ Income * Population, data = states)
> 
> # Plot marginal effect of Income across the observed range of Population
> # on the Murder rate
> plot_me(m1, 'Income', 'Population', ci = 95)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PlotPrjNetworks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GanttChart
> ### Title: GanttChart
> ### Aliases: GanttChart
> 
> ### ** Examples
> 
> project1=data.frame(
+     task=c("Market Research","Concept Development","Viability Test",
+ "Preliminary Design","Process Design","Prototyping","Market Testing","Final Design",
+ "Launching"),
+     start=c("2015-07-05","2015-07-05","2015-08-05","2015-10-05","2015-10-05","2016-02-18",
+ "2016-03-18","2016-05-18","2016-07-18"),
+     end=c("2015-08-05","2015-08-05","2015-10-05","2016-01-05","2016-02-18","2016-03-18",
+ "2016-05-18","2016-07-18","2016-09-18"))
> project2=data.frame(
+     from=c(1,2,3,4,5,6,7,8),
+     to=c(2,3,4,5,6,7,8,9),
+     type=c("SS","FS","FS","SS","FS","FS","FS","FS"),
+     delay=c(7,7,7,8,10,10,10,10))
> GanttChart(project1,project2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘plotROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeomRoc
> ### Title: Empirical Receiver Operating Characteristic Curve
> ### Aliases: GeomRoc geom_roc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> D.ex <- rbinom(50, 1, .5)
> rocdata <- data.frame(D = c(D.ex, D.ex), 
+                    M = c(rnorm(50, mean = D.ex, sd = .4), rnorm(50, mean = D.ex, sd = 1)), 
+                    Z = c(rep("A", 50), rep("B", 50)))
> 
> ggplot(rocdata, aes(m = M, d = D)) + geom_roc()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 99-101 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bivarplots
> ### Title: Plots the bivariate relationship between two measures for each
> ###   group/unit
> ### Aliases: bivarplots
> 
> ### ** Examples
> 
> a <- runif(1000, min = 0, max = 1)
> b <- a + rnorm(1000, mean = 0, sd = 1)
> c <- rep(c(1:10), times = 100)
> data <- data.frame(a, b, c)
> bivarplots("a", "b", "c", data)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: bivarplots ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotrr-vignette.Rmd’ using rmarkdown
Quitting from lines 30-36 (plotrr-vignette.Rmd) 
Error: processing vignette 'plotrr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotrr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plspm_introduction.Rnw’ using knitr

Attaching package: 'ggplot2'

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

    alpha

Quitting from lines 310-329 (plspm_introduction.Rnw) 
Error: processing vignette 'plspm_introduction.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plspm_introduction.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plte_plot
> ### Title: Plot objects created by plte_builder
> ### Aliases: plte_plot
> 
> ### ** Examples
> 
> data('negative')
> 
> # BTSCS set the data
> neg_set <- btscs(df = negative, event = 'y', t_var = 'tim',
+                  cs_unit = 'group', pad_ts = FALSE)
>                  # Create temporal dependence variables
> neg_set$t <- neg_set$spell + 1
> 
> m1 <- glm(y ~ x + t + I(t^2) + I(t^3),
+           family = binomial(link = 'logit'),
+           data = neg_set)
> 
> counterfactual <- data.frame(x = 0.5)
> 
> sim1 <- plte_builder(obj = m1, obj_tvar = 't',
+                      cf = counterfactual, t_points = c(13, 25),
+                      cf_duration = 4, ci = 99)
> 
> # With time point labels
> plte_plot(sim1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PMmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pl.histgg
> ### Title: Plot histograms for a data frame with ggplot2
> ### Aliases: pl.histgg
> 
> ### ** Examples
> 
> pl.histgg(as.data.frame(EuStockMarkets),1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pl.histgg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pmpp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pmpp
> ### Title: Plot method for objects of class 'pmpp'.
> ### Aliases: plot.pmpp
> 
> ### ** Examples
> 
> data(EmplUK, package = "plm")
> EmplUK <- dplyr::filter(EmplUK, year %in% c(1978, 1979, 1980, 1981, 1982))
> pmpp_model <- pmpp(dep_var = "emp", data = EmplUK)
> plot(pmpp_model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘POCRE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pocre
> ### Title: Visualization of a 'pocre' Object
> ### Aliases: plot.pocre
> 
> ### ** Examples
> 
> data(simdata)
> xx <- scale(as.matrix(simdata[,-1]))
> yy <- scale(as.matrix(simdata[,1]))
> 
> ##Fit with pocre()
> pres <- pocre(yy, xx, lambda=0.9)
.....
> 
> # plot(pres,which=1)
> plot(pres)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PointFore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate.functional
> ### Title: Estimate Functional
> ### Aliases: estimate.functional
> 
> ### ** Examples
> 
> # estimate constant quantile level of GDP forecast
> res <- estimate.functional(Y=GDP$observation, X=GDP$forecast,
+ model=constant)
Drop  1 case(s) because of chosen instruments
Choose parameter theta0 automatically.
> summary(res)
$call
estimate.functional(model = constant, Y = GDP$observation, X = GDP$forecast)

$coefficients
          Estimate Std. Error  t value     Pr(>|t|)
Theta[1] 0.5980637 0.04429534 13.50173 1.527435e-41

$Jtest

 ##  J-Test: degrees of freedom is 2  ## 

                J-test    P-value 
Test E(g)=0:    5.507506  0.063688


> plot(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GDP.Rmd’ using rmarkdown
Quitting from lines 26-35 (GDP.Rmd) 
Error: processing vignette 'GDP.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GDP.Rmd’

--- re-building ‘Precipitation.Rmd’ using rmarkdown
Quitting from lines 26-38 (Precipitation.Rmd) 
Error: processing vignette 'Precipitation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Precipitation.Rmd’

--- re-building ‘Tutorial.Rmd’ using rmarkdown
Quitting from lines 95-97 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘GDP.Rmd’ ‘Precipitation.Rmd’ ‘Tutorial.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: event.plot
> ### Title: Plot event years for individual trees
> ### Aliases: event.plot
> 
> ### ** Examples
> 
> ## Plot event years from pointer.rgc output
> data(s033)
> py <- pointer.rgc(s033)
> event.plot(py, start.yr = 1950, end.yr = NULL) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pointRes_functionality.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 58-59 (pointRes_functionality.Rmd) 
Error: processing vignette 'pointRes_functionality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pointRes_functionality.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: politenessPlot
> ### Title: Politeness plot
> ### Aliases: politenessPlot
> 
> ### ** Examples
> 
> 
> data("phone_offers")
> 
> polite.data<-politeness(phone_offers$message, parser="none", binary=FALSE, drop_blank=FALSE)
Warning: argument binary is deprecated; please use metric instead.
Note: Some features cannot be computed without part-of-speech tagging. See ?spacyr::spacyr for details.> 
> politeness::politenessPlot(polite.data,
+                            split=phone_offers$condition,
+                            split_levels = c("Tough","Warm"),
+                            split_name = "Condition",
+                            top_title = "Average Feature Counts")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘politeness.Rmd’ using rmarkdown
politeness v0.2.6 successfully loaded. See ?politeness for help.
Quitting from lines 105-109 (politeness.Rmd) 
Error: processing vignette 'politeness.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘politeness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Parsed with column specification:
cols(
  Favorable = col_double(),
  Unfavorable = col_double(),
  Undecided = col_double(),
  poll_slug = col_character(),
  survey_house = col_character(),
  start_date = col_date(format = ""),
  end_date = col_date(format = ""),
  question_text = col_character(),
  sample_subpopulation = col_character(),
  observations = col_double(),
  margin_of_error = col_double(),
  mode = col_character(),
  partisanship = col_character(),
  partisan_affiliation = col_character()
)
Parsed with column specification:
cols(
  label = col_character(),
  date = col_date(format = ""),
  value = col_double(),
  low = col_logical(),
  high = col_logical()
)
Quitting from lines 36-46 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: poly_plot
> ### Title: Plot a polynomial matrix
> ### Aliases: poly_plot poly_plot_data
> 
> ### ** Examples
> 
> # Defaults to plotting using the row number as x-axis
> m <- poly(1:100, degree = 3)
> poly_plot(m)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 68-69 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_iRAM_dist
> ### Title: Plot distribution of recovery time based on bootstrapped version
> ###   of iRAM
> ### Aliases: plot_iRAM_dist
> 
> ### ** Examples
> 
> ## Don't show: 
> plot_iRAM_dist(bootstrap_iRAM_3node$recovery.time.reps)
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_iRAM_dist ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Three_node_exmaple.Rmd’ using rmarkdown
Loading required package: reshape2
Quitting from lines 120-156 (Three_node_exmaple.Rmd) 
Error: processing vignette 'Three_node_exmaple.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Three_node_exmaple.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_dfa
> ### Title: Plot Log-OR vs. X for Normal Discriminant Function Approach
> ### Aliases: plot_dfa
> 
> ### ** Examples
> 
> # Fit discriminant function model for poolwise Xtilde vs. (Y, C), without
> # assuming a constant log-OR. Ignoring processing errors for simplicity.
> data(pdat1)
> fit <- p_dfa_xerrors(g = pdat1$g, y = pdat1$numcases, xtilde = pdat1$xtilde,
+                      c = pdat1$c, errors = "neither", constant_or = FALSE)
> 
> # Plot estimated log-OR vs. X at mean value for C
> p <- plot_dfa(estimates = fit$estimates, varcov = fit$theta.var,
+               xrange = range(pdat1$xtilde / pdat1$g),
+               cvals = mean(pdat1$c / pdat1$g))
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
> p
Warning: Removed 1 rows containing missing values (geom_hline).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 169-172 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

--- re-building ‘intro-poped.Rmd’ using rmarkdown
Quitting from lines 155-156 (intro-poped.Rmd) 
Error: processing vignette 'intro-poped.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-poped.Rmd’

SUMMARY: processing the following files failed:
  ‘examples.Rmd’ ‘intro-poped.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diversity_ci
> ### Title: Perform bootstrap statistics, calculate, and plot confidence
> ###   intervals.
> ### Aliases: diversity_ci
> 
> ### ** Examples
> 
> library(poppr)
> data(Pinf)
> diversity_ci(Pinf, n = 100L)

Confidence Intervals have been centered around observed statistic.
Please see ?diversity_ci for details.

Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: diversity_ci ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlg.Rmd’ using rmarkdown
Loading required package: adegenet
Loading required package: ade4

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

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


This is poppr version 2.8.2. To get started, type package?poppr
OMP parallel support: available
Loading required package: ape

Attaching package: 'phangorn'

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

    AICc

Quitting from lines 289-294 (mlg.Rmd) 
Error: processing vignette 'mlg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mlg.Rmd’

--- re-building ‘poppr_manual.Rmd’ using rmarkdown
Quitting from lines 845-848 (poppr_manual.Rmd) 
Error: processing vignette 'poppr_manual.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘poppr_manual.Rmd’

--- re-building ‘algo.Rnw’ using knitr
Loading required package: adegenet
Loading required package: ade4

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

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


This is poppr version 2.8.2. To get started, type package?poppr
OMP parallel support: available
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
--- finished re-building ‘algo.Rnw’

SUMMARY: processing the following files failed:
  ‘mlg.Rmd’ ‘poppr_manual.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 45-46 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘burkina-faso-females.Rnw’ using Sweave
Loading required package: coda
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files
gdata: ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files
gdata: ENABLED.

Attaching package: ‘gdata’

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

    nobs

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

    object.size

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

    startsWith


Error: processing vignette 'burkina-faso-females.Rnw' failed with diagnostics:
 chunk 8 (label = PLOT-age-specific-fert-rate) 
Error in Summary.unit(structure(c(3.6, 3.6), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘burkina-faso-females.Rnw’

SUMMARY: processing the following file failed:
  ‘burkina-faso-females.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map.marginal
> ### Title: Plot Marginal Distribution
> ### Aliases: map.marginal
> 
> ### ** Examples
> 
> data(iris)
> 
> ## set data frame and labels
> df <- subset(iris,select=-Species)
> labels <- subset(iris,select=Species)
> 
> ## build a map
> m <- map.build(df, labels, xdim=15, ydim=10, train=1000)
> 
> ## display marginal distribution of dimension 1
> map.marginal(m,1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-zoned.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    collapse

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 139-150 (getting-zoned.Rmd) 
Error: processing vignette 'getting-zoned.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-zoned.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-zoned.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘powdR_vignette.Rmd’ using rmarkdown
powdR: Full Pattern Summation of X-Ray Powder Diffraction Data
Quitting from lines 42-56 (powdR_vignette.Rmd) 
Error: processing vignette 'powdR_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘powdR_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dropout_manual
> ### Title: Manually specify dropout per time point
> ### Aliases: dropout_manual
> 
> ### ** Examples
> 
> dropout <- dropout_manual(0, 0, 0, 0, 0.2, 0.2, 0.3, 0.3, 0.4, 0.4, 0.45)
> 
> p <- study_parameters(n1 = 11,
+                       n2 = 5,
+                       n3 = 6,
+                       T_end = 10,
+                       icc_pre_subject = 0.5,
+                       icc_pre_cluster = 0,
+                       var_ratio = 0.03,
+                       icc_slope = 0.05,
+                       dropout = dropout,
+                       cohend = -0.8)
> plot(p, plot = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulations.Rmd’ using rmarkdown
--- finished re-building ‘simulations.Rmd’

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

--- re-building ‘three-level.Rmd’ using rmarkdown
Scale for 'x' is already present. Adding another scale for 'x', which
will replace the existing scale.
Quitting from lines 197-200 (three-level.Rmd) 
Error: processing vignette 'three-level.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘three-level.Rmd’

--- re-building ‘two-level.Rmd’ using rmarkdown
Quitting from lines 163-164 (two-level.Rmd) 
Error: processing vignette 'two-level.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘two-level.Rmd’

SUMMARY: processing the following files failed:
  ‘three-level.Rmd’ ‘two-level.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fcm.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 202-207 (fcm.Rmd) 
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fcm.Rmd’

--- re-building ‘pcm.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 188-193 (pcm.Rmd) 
Error: processing vignette 'pcm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pcm.Rmd’

--- re-building ‘upfc.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 235-240 (upfc.Rmd) 
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘upfc.Rmd’

SUMMARY: processing the following files failed:
  ‘fcm.Rmd’ ‘pcm.Rmd’ ‘upfc.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCity
> ### Title: Visualizatio of all top cities.
> ### Aliases: plotCity
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> ## Don't show: 
> library(ppcSpatial)
> plotCity()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PPforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ternary_str
> ### Title: Data structure with the projected and boundary by node and
> ###   class.
> ### Aliases: ternary_str
> 
> ### ** Examples
> 
> #crab data set with all the observations used as training
> pprf.crab <- PPforest(data = crab, std =TRUE, class = "Type",
+  size.tr = 1, m = 100, size.p = .5, PPmethod = 'LDA')
>  require(dplyr)
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

> pl_ter <- function(dat, dx, dy ){
+   p1  <- dat[[1]] %>% dplyr::filter(pair %in% paste(dx, dy, sep = "-") ) %>%
+     dplyr::select(Class, x, y) %>%
+     ggplot2::ggplot(ggplot2::aes(x, y, color = Class)) +
+     ggplot2::geom_segment(data = dat[[2]], ggplot2::aes(x = x1, xend = x2,
+                                                y = y1, yend = y2), color = "black" ) +
+     ggplot2::geom_point(size = I(3), alpha = .5) +
+     ggplot2::labs(y = " ",  x = " ") +
+     ggplot2::theme(legend.position = "none", aspect.ratio = 1) +
+     ggplot2::scale_colour_brewer(type = "qual", palette = "Dark2") +
+     ggplot2::labs(x = paste0("T", dx, " "), y = paste0("T", dy, " ")) +
+     ggplot2::theme(aspect.ratio = 1)
+   p1
+ }
> #ternary plot in tree different selected dierections
>  pl_ter(ternary_str(pprf.crab, id = c(1, 2, 3), sp = 3, dx = 1, dy = 2), 1, 2 )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPforest-vignette.Rmd’ using rmarkdown
Loading required package: PPforest
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: RColorBrewer
Loading required package: GGally
Loading required package: ggplot2

Attaching package: 'GGally'

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

    nasa

Loading required package: gridExtra

Attaching package: 'gridExtra'

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

    combine

Loading required package: PPtreeViz
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Quitting from lines 118-129 (PPforest-vignette.Rmd) 
Error: processing vignette 'PPforest-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PPforest-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ppgmmga
> ### Title: Projection pursuit based on Gaussian mixtures and evolutionary
> ###   algorithms for data visualisation
> ### Aliases: ppgmmga print.ppgmmga
> 
> ### ** Examples
> 
> 
> data(iris)
> X <- iris[,-5]
> Class <- iris$Species
> 
> # Unscented Transformation approximation (default)
> pp1 <- ppgmmga(data = X, d = 2, approx = "UT", seed = 123)
> summary(pp1, check = TRUE)
── ppgmmga ───────────────────────────── 

Data dimensions               = 150 x 4 
Data transformation           = center & scale 
Projection subspace dimension = 2 
GMM density estimate          = (VVV,2)
Negentropy approximation      = UT 
GA optimal negentropy         = 0.9461873 
GA encoded basis solution: 
          x1       x2         x3       x4       x5       x6
[1,] 1.62551 1.170375 0.07635218 0.564489 1.355774 2.316635

Estimated projection basis: 
                     PP1        PP2
Sepal.Length -0.07013906 -0.4841843
Sepal.Width   0.00384141 -0.6982979
Petal.Length -0.91821379  0.2345145
Petal.Width  -0.38980661 -0.4721744

Monte Carlo Negentropy approximation check: 
                           UT
Approx Negentropy 0.946187289
MC Negentropy     0.943898857
MC se             0.003331479
Relative accuracy 1.002424446
> plot(pp1, Class)
Warning in if (params$x != 0) { :
  the condition has length > 1 and only the first element will be used
Warning in if (params$y != 0) { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ppgmmga.Rmd’ using rmarkdown
Package 'ppgmmga' version 1.0.1
Quitting from lines 58-63 (ppgmmga.Rmd) 
Error: processing vignette 'ppgmmga.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ppgmmga.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PPQ.ggplot
> ### Title: Heatmap/Contour GGPlot for Dynamically Assessing Power of the
> ###   CQA PPQ Plan Using General Multiplier.
> ### Aliases: PPQ.ggplot
> 
> ### ** Examples
> 
> mu <- seq(95, 105, 0.1)
> sigma <- seq(0.1,1.7,0.1)
> PPQ.ggplot(attr.name = "Sterile Concentration Assay", attr.unit = "%", Llim=95, Ulim=105,
+ mu = mu, sigma = sigma, k=2.373, dynamic = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Quitting from lines 114-120 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PPQplan-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Huberplot
> ### Title: Huber plot
> ### Aliases: Huberplot
> ### Keywords: projection pursuit
> 
> ### ** Examples
> 
> data(iris)
> Huberplot(iris[,1:2],iris[,5],PPmethod="LDA")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Huberplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘prcbench-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.evalcurve
> ### Title: Plot the result of Precision-Recall curve evaluation
> ### Aliases: autoplot.evalcurve
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ## Plot evaluation results on test datasets r1, r2, and r3
> testset <- create_testset("curve", c("c1", "c2", "c3"))
> toolset <- create_toolset(set_names = "crv5")
> eres1 <- run_evalcurve(testset, toolset)
> autoplot(eres1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: autoplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [205s/217s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(prcbench)
  > 
  > test_check("prcbench")
  ── 1. Failure: autoplot.evalcurve (@test_plot_autoplot.R#16)  ──────────────────
  `suppressWarnings(autoplot(evalcrv1))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ── 2. Failure: autoplot.evalcurve (@test_plot_autoplot.R#22)  ──────────────────
  `suppressWarnings(autoplot(evalcrv2))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ── 3. Failure: autoplot.evalcurve ret_grob (@test_plot_autoplot.R#36)  ─────────
  `suppressWarnings(grid.draw(pp))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 752 SKIPPED: 0 FAILED: 3
  1. Failure: autoplot.evalcurve (@test_plot_autoplot.R#16) 
  2. Failure: autoplot.evalcurve (@test_plot_autoplot.R#22) 
  3. Failure: autoplot.evalcurve ret_grob (@test_plot_autoplot.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 156-169 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_r_squared
> ### Title: Plot R^2 (r-squared) values for a range of number of profiles
> ### Aliases: plot_r_squared
> 
> ### ** Examples
> 
> df <- mtcars
> plot_r_squared(df, mpg, wt, hp, qsec, to_center = TRUE, lower_bound = 2, upper_bound = 4)
################################
Clustering data for iteration 2
Clustering data for iteration 3
Clustering data for iteration 4
################################
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_r_squared
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_prcr.Rmd’ using rmarkdown
Quitting from lines 23-37 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction_to_prcr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pplot.deciles
> ### Title: Plot deciles
> ### Aliases: pplot.deciles precintcon.plot.deciles
> ### Keywords: deciles precipitation
> 
> ### ** Examples
> 
> ## Loading the monthly precipitation serie.
> #
> data(monthly)
> 
> ## Performing the a set of statistical analysis
> #
> pplot.deciles(monthly)
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pplot.deciles ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 61-69 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 46-49 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘predict3d.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DimensionRed
> ### Title: Generic Dimensionallity Reduction Function
> ### Aliases: DimensionRed
> 
> ### ** Examples
> 
> # reducing dimension of Grip aperture from 10 to 2
> GripAperture <- DimensionRed(KinData,selectedCols = 12:21,
+ outcome = KinData[,"Object.Size"],plot = TRUE)

Performing Dimensionality Reduction analysis 

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DimensionRed ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘preference-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.preference.trial
> ### Title: Plot the effect sizes of a preference trial
> ### Aliases: plot.preference.trial
> 
> ### ** Examples
> 
> 
> # Plot trials with fixed power and varying preference effect.
> trials <- pt_from_power(power = 0.8, pref_effect = seq(0.5, 2, by = 0.1), 
+                         selection_effect = 1, treatment_effect = 1, 
+                         sigma2 = 1, pref_prop = 0.6)
> plot(trials)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘prepplotOverview.Rmd’ using rmarkdown
Quitting from lines 31-62 (prepplotOverview.Rmd) 
Error: processing vignette 'prepplotOverview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘prepplotOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘preprosim.Rmd’ using rmarkdown
Loading required package: lattice
Loading required package: ggplot2
Warning: Continuous x aesthetic -- did you forget aes(group=...)?
Quitting from lines 63-65 (preprosim.Rmd) 
Error: processing vignette 'preprosim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘preprosim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘preproviz.Rmd’ using rmarkdown
Quitting from lines 35-37 (preproviz.Rmd) 
Error: processing vignette 'preproviz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘preproviz.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_preText.Rmd’ using rmarkdown
Quitting from lines 140-141 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting_started_with_preText.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sigplot
> ### Title: sigplot
> ### Aliases: sigplot
> 
> ### ** Examples
> 
> 
> #Load the iris dataset
> data(iris)
> 
> #Set up the predictors object
> 
> predictors=iris[,c(1:4)]
> colnames(predictors)<-colnames(iris[1:4])
> 
> #Execute the main pRF function
> p.test<-pRF(response=factor(iris$Species),
+ predictors=iris[,c(1:4)],n.perms=20,mtry=3,
+ type="classification",alpha=0.05)
Checking if response variable is valid
fitting original random forest
populating permuted importance table
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
calculating permutation p.values
adjusting for FDR using two-step BH
> 
> #Plot
> 
> sigplot(pRF.list=p.test,threshold=0.1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘interpolation-in-small-samples.Rmd’ using rmarkdown
Quitting from lines 50-91 (interpolation-in-small-samples.Rmd) 
Error: processing vignette 'interpolation-in-small-samples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interpolation-in-small-samples.Rmd’

--- re-building ‘visualizing-psm-results.Rmd’ using rmarkdown
Quitting from lines 83-147 (visualizing-psm-results.Rmd) 
Error: processing vignette 'visualizing-psm-results.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘visualizing-psm-results.Rmd’

SUMMARY: processing the following files failed:
  ‘interpolation-in-small-samples.Rmd’ ‘visualizing-psm-results.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.primerTree
> ### Title: plot function for a primerTree object, calls plot_tree_ranks
> ### Aliases: plot.primerTree
> 
> ### ** Examples
> 
> library(gridExtra)
> library(directlabels)
> #plot with all common ranks
> plot(mammals_16S)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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-patched-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘equivocal-zones.Rmd’ using rmarkdown

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

--- finished re-building ‘equivocal-zones.Rmd’

--- re-building ‘where-to-use.Rmd’ using rmarkdown

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

Loading required package: tidyr
Quitting from lines 170-196 (where-to-use.Rmd) 
Error: processing vignette 'where-to-use.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘where-to-use.Rmd’

SUMMARY: processing the following file failed:
  ‘where-to-use.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggroc.roc
> ### Title: Plot a ROC curve with ggplot2
> ### Aliases: ggroc.roc ggroc.list ggroc
> 
> ### ** Examples
> 
> # Create a basic roc object
> data(aSAH)
> rocobj <- roc(aSAH$outcome, aSAH$s100b)
> rocobj2 <- roc(aSAH$outcome, aSAH$wfns)
> 
> library(ggplot2)
> g <- ggroc(rocobj)
> g
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘productplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prodplot
> ### Title: Create a product plot
> ### Aliases: prodplot
> 
> ### ** Examples
> 
> if (require("ggplot2")) {
+ prodplot(happy, ~ happy, "hbar")
+ prodplot(happy, ~ happy, "hspine")
+ 
+ prodplot(happy, ~ sex + happy, c("vspine", "hbar"))
+ prodplot(happy, ~ sex + happy, stacked())
+ 
+ prodplot(happy, ~ happy + sex | health, mosaic("h")) + aes(fill=happy)
+ # The levels argument can be used to extract a given level of the plot
+ prodplot(happy, ~ sex + happy, stacked(), level = 1)
+ prodplot(happy, ~ sex + happy, stacked(), level = 2)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘profr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.profr
> ### Title: Visualise profiling data with ggplot2. Visualise profiling data
> ###   stored in a 'profr' data.frame.
> ### Aliases: ggplot.profr
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require("ggplot2")) {
+   ggplot(nesting_prof)
+   ggplot(reshape_prof)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘projections-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumulate.projections
> ### Title: Compute cumulative projections
> ### Aliases: cumulate.projections
> 
> ### ** Examples
> 
> 
> if (require(distcrete) &&
+     require(incidence)) {
+ 
+   ## simulate basic epicurve
+   dat <- c(0, 2, 2, 3, 3, 5, 5, 5, 6, 6, 6, 6)
+   i <- incidence(dat)
+ 
+ 
+   ## example with a function for SI
+   si <- distcrete("gamma", interval = 1L,
+                   shape = 1.5,
+                   scale = 2, w = 0)
+   set.seed(1)
+   pred_1 <- project(i, runif(100, 0.8, 1.9), si, n_days = 30)
+   plot_1 <- plot(pred_1)
+ 
+   ## cumulative predictions
+   pred_1_cum <- cumulate(pred_1)
+   pred_1_cum
+   plot(pred_1_cum)
+ }
Loading required package: distcrete
Loading required package: incidence
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
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().
This is projpred version 1.1.1.
This is bayesplot version 1.6.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Quitting from lines 62-64 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
Loading required package: Rcpp
Loading required package: rlang

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 51-52 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quick_start.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotciAAS
> ### Title: Plot of CI estimation of adjusted ArcSine
> ### Aliases: PlotciAAS
> 
> ### ** Examples
> 
> n=5; alp=0.05;h=2
> PlotciAAS(n,alp,h)
Warning: Ignoring unknown aesthetics: x
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRROC.Rnw’ using Sweave
Error: processing vignette 'PRROC.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PRROC.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distanceScores
> ### Title: Calculate distance scores on data in preparation for composite
> ###   scoring
> ### Aliases: distanceScores
> 
> ### ** Examples
> 
> # this example creates distances for the built in mtcars data
> # see ?mtcars for more details
> # The distances are calculated from the "best" in the dataset
> # defined by these thresholds
> thresholds <- with(mtcars, c(
+   mpg = max(mpg),
+   hp = max(hp),
+   wt = min(wt),
+   qsec = min(qsec)))
> 
> # higher mpg and hp are better,
> # whereas lower wt and qsec are better
> dres <- distanceScores(mtcars[, c("mpg", "hp", "wt", "qsec")],
+   thresholds = list(thresholds),
+   higherisbetter = c(TRUE, TRUE, FALSE, FALSE),
+   saveall = TRUE)
> 
> # see a density plot of the distance scores
> dres$Density
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘psda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pplot
> ### Title: Plot polygonal symbolic variable
> ### Aliases: pplot
> 
> ### ** Examples
> 
> x <- psim(10, 10) #simulate 10 polygons of 10 sides
> pplot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 403-408 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pstr-vignette.Rmd’ using rmarkdown
Quitting from lines 129-132 (pstr-vignette.Rmd) 
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pstr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 668-680 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘loo::kfold’ by ‘rstanarm::kfold’ when loading ‘psycho’
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/psycho.Rcheck/00install.out’ for details.
Running examples in ‘psycho-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDI
> ### Title: Highest Density Intervals (HDI).
> ### Aliases: HDI
> 
> ### ** Examples
> 
> library(psycho)
> 
> distribution <- rnorm(1000, 0, 1)
> HDI_values <- HDI(distribution)
> print(HDI_values)
95% CI [-2.10, 2.03]
> plot(HDI_values)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘psychotree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bttree
> ### Title: Bradley-Terry Trees
> ### Aliases: bttree plot.bttree print.bttree predict.bttree itempar.bttree
> ### Keywords: tree
> 
> ### ** Examples
> 
> o <- options(digits = 4)
> 
> ## Germany's Next Topmodel 2007 data
> data("Topmodel2007", package = "psychotree")
> 
> ## BT tree
> tm_tree <- bttree(preference ~ ., data = Topmodel2007, minsize = 5, ref = "Barbara")
> plot(tm_tree, abbreviate = 1, yscale = c(0, 0.5))
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Errors in running code in vignettes:
when running code in ‘raschtree.Rnw’
  ...

> library("psychotree")
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: psychotools

> data("SPISA", package = "psychotree")

> if (file.exists("raschtree-spisa.rda")) load("raschtree-spisa.rda") else {
+     my_first_raschtree <- raschtree(spisa ~ age + gender + semester + 
 .... [TRUNCATED] 

> file.remove("raschtree-spisa.rda")
[1] TRUE

> plot(my_first_raschtree)

  When sourcing ‘raschtree.R’:
Error: no string supplied for 'strwidth/height' unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘raschtree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: psychotools

Error: processing vignette 'raschtree.Rnw' failed with diagnostics:
 chunk 9 (label = plot_raschtree) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘raschtree.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_CalibratedMSErr
> ### Title: Plot bargraph of uncalibrated mass errors for each Raw file.
> ### Aliases: plot_CalibratedMSErr
> 
> ### ** Examples
> 
>   n = c(150, 1000, 1000, 1000)
>   data = data.frame(fc.raw.file = repEach(letters[4:1], n),
+                     mass.error..ppm. = c(rnorm(n[1], 1, 2.4),
+                                          rnorm(n[2], 0.5, 0.5),
+                                          rnorm(n[3], 0.1, 0.7),
+                                          rnorm(n[4], 0.3, 0.8)))
>   stats = data.frame(fc.raw.file = letters[4:1],
+                      sd = c(2.4, 0.5, 0.7, 0.8),
+                      outOfCal = c(TRUE, FALSE, FALSE, FALSE))           
>   plot_CalibratedMSErr(data, MQBug_raw_files = letters[1], stats, y_lim = c(-20,20), 15, "subtitle")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pwr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.power.htest
> ### Title: Plot diagram of sample size vs. test power
> ### Aliases: plot.power.htest
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## Two-sample t-test
> p.t.two <- pwr.t.test(d=0.3, power=0.8, type="two.sample", alternative="two.sided")
> plot(p.t.two)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pwr-vignette.Rmd’ using rmarkdown
Quitting from lines 62-67 (pwr-vignette.Rmd) 
Error: processing vignette 'pwr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pwr-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_density
> ### Title: Plot density of empirical checkerboard copula
> ### Aliases: plot_density
> 
> ### ** Examples
> 
> n <- 1000
> x <- runif(n,0,1)
> y <- runif(n,0,1)
> sample <- data.frame(x,y)
> plot(sample)
> 
> mass <- emp_c_copula(sample, resolution=8)
> plot_density(mass, density=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘QCAtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot
> ### Title: Plot fuzzy set score of two sets against each other
> ### Aliases: xyplot
> 
> ### ** Examples
> 
> require(QCA)
Loading required package: QCA

To cite this package in publications, please use:
  Dusa, Adrian (2019) QCA with R. A Comprehensive Resource.
  Springer International Publishing.

To run the graphical user interface, use: runGUI()

NOTE: Found multiple functions and object type conflicts in the fork package QCApro.
      To avoid confusion, please uninstall it before using this software, with:
      uninstall("QCApro")

> data(d.urban)
> xyplot("MLC", "WSR", d.urban)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘qcQpcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qcQpcr-package
> ### Title: Histone ChIP-Seq qPCR Analyzer Histone ChIP-Seq qPCR Analyzer
> ### Aliases: qcQpcr-package
> ### Keywords: qpcr
> 
> ### ** Examples
> 
> 
> 
>   library(ggplot2)
>   data(SampleTest)
>   qcQpcr(SampleTest,'Title for your graph')
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘QCSimulator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SWAPQ0Q1
> ### Title: SWAP Q0 Q1
> ### Aliases: SWAPQ0Q1
> 
> ### ** Examples
> 
> # Initialze global variables
> init()
> SWAPQ0Q1(q110_)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘qdap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: type_token_ratio
> ### Title: Type-Token Ratio
> ### Aliases: type_token_ratio
> 
> ### ** Examples
> 
> with(raj, type_token_ratio(dialogue, person))
            person   wc   ttr
1            Nurse 2206 0.426
2     Lady Capulet  872 0.436
3           Juliet 4263 0.454
4            Romeo 4665 0.462
5   Friar Laurence 2727 0.470
6          Abraham   24 0.500
7          Sampson  259 0.502
8            Paris  539 0.509
9          Capulet 2123 0.509
10           Peter  245 0.510
11          Prince  585 0.520
12        Mercutio 2094 0.533
13         Servant  183 0.573
14          Tybalt  262 0.574
15       Balthasar  232 0.575
16        Benvolio 1153 0.582
17        Montague  316 0.641
18         Gregory  149 0.664
19   First Servant   79 0.679
20  First Watchman  134 0.679
21  Second Capulet   17 0.706
22            Page   81 0.728
23          Chorus  113 0.730
24      Friar John   96 0.735
25  Second Servant   96 0.740
26   First Citizen   43 0.744
27  First Musician   62 0.750
28 Second Musician   34 0.824
29  Third Watchman   26 0.846
30      Apothecary   53 0.849
31   Lady Montague   28 0.897
32        Musician    8 1.000
33 Second Watchman    9 1.000
34  Third Musician    7 1.000

Type-token ratio for entire text: 0.448
> plot(with(raj, type_token_ratio(dialogue, person)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘qgcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.qgcompfit
> ### Title: plot.qgcompfit: default plotting method for a qgcompfit object
> ### Aliases: plot.qgcompfit
> 
> ### ** Examples
> 
> set.seed(12)
> dat <- data.frame(x1=(x1 <- runif(100)), x2=runif(100), x3=runif(100), z=runif(100),
+                   y=runif(100)+x1+x1^2)
> ft <- qgcomp.noboot(y ~ z + x1 + x2 + x3, expnms=c('x1','x2','x3'), data=dat, q=4)
> ft
Scaled effect size (positive direction, sum of positive coefficients = 0.515)
    x1     x2 
0.9759 0.0241 

Scaled effect size (negative direction, sum of negative coefficients = -0.0163)
x3 
 1 

Mixture slope parameters (Delta method CI):

     Estimate Std. Error Lower CI Upper CI t value Pr(>|t|)
psi1 0.499201   0.050285  0.40064  0.59776  9.9275 2.22e-16
> plot(ft)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qgcomp-vignette.Rmd’ using knitr
Loading required package: ggplot2
Loading required package: grid
Loading required package: gridExtra
Quitting from lines 171-186 (qgcomp-vignette.Rmd) 
Error: processing vignette 'qgcomp-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qgcomp-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘qicharts2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: paretochart
> ### Title: Paretochart
> ### Aliases: paretochart
> 
> ### ** Examples
> 
> # Generate categorical vector
> x <- rep(LETTERS[1:9], c(256, 128, 64, 32, 16, 8, 4, 2, 1))
> 
> # Make paretochart
> paretochart(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qicharts2.Rmd’ using rmarkdown
Quitting from lines 33-39 (qicharts2.Rmd) 
Error: processing vignette 'qicharts2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qicharts2.Rmd’

SUMMARY: processing the following file failed:
  ‘qicharts2.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.tcc
> ### Title: Summarise Trellis Control Charts
> ### Aliases: summary.tcc
> 
> ### ** Examples
> 
> # Build data frame for example
> d <- data.frame(x = rep(1:24, 4),
+                 mo = (rep(seq(as.Date('2014-1-1'),
+                               length.out = 24,
+                               by = 'month'),
+                           4)),
+                 n = rbinom(4 * 24, 100, 0.5),
+                 d = round(runif(4 * 24, 90, 110)),
+                 g1 = rep(c('a', 'b'), each = 48),
+                 g2 = rep(c('A', 'B'), each = 24))
> 
> # P chart
> p <- tcc(n, d, mo, g1 = g1, g2 = g2, breaks = 12, data = d, chart = 'p')
> plot(p)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘qqplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_pp_band
> ### Title: Probability-probability confidence bands
> ### Aliases: stat_pp_band
> 
> ### ** Examples
> 
> # generate random Normal data
> set.seed(0)
> smp <- data.frame(norm = rnorm(100), exp = rexp(100))
> 
> # Normal P-P plot of Normal data
> gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
+  stat_pp_band() +
+  stat_pp_line() +
+  stat_pp_point() +
+  labs(x = "Probability Points", y = "Cumulative Probability")
> gg
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: qqplotr
Loading required package: ggplot2

Attaching package: 'qqplotr'

The following objects are masked from 'package:ggplot2':

    StatQqLine, stat_qq_line

Quitting from lines 101-107 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bounded.reg
> ### Title: Fit a linear model with infinity-norm plus ridge-like
> ###   regularization
> ### Aliases: bounded.reg
> ### Keywords: models, regression
> 
> ### ** Examples
> 
> ## Simulating multivariate Gaussian with blockwise correlation
> ## and piecewise constant vector of parameters
> beta <- rep(c(0,1,0,-1,0), c(25,10,25,10,25))
> cor <- 0.75
> Soo <- toeplitz(cor^(0:(25-1))) ## Toeplitz correlation for irrelevant variables
> Sww  <- matrix(cor,10,10) ## bloc correlation between active variables
> Sigma <- bdiag(Soo,Sww,Soo,Sww,Soo)
> diag(Sigma) <- 1
> n <- 50
> x <- as.matrix(matrix(rnorm(95*n),n,95) %*% chol(Sigma))
> y <- 10 + x %*% beta + rnorm(n,0,10)
> 
> ## Infinity norm without/with an additional l2 regularization term
> ## and with structuring prior
> labels <- rep("irrelevant", length(beta))
> labels[beta != 0] <- "relevant"
> plot(bounded.reg(x,y,lambda2=0) , label=labels) ## a mess
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘QualInt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QualInt-package
> ### Title: R-package for qualitative interaction test
> ### Aliases: QualInt-package
> 
> ### ** Examples
> 
> test9 <- qualval(effect = c(1.0, 0.5, -2.0), se = c(0.86, 0.64, 0.32))
> print(test9)

Call:
qualval(effect = c(1, 0.5, -2), se = c(0.86, 0.64, 0.32))

Type:
unknown

Estimating Results for treatment effects:
  Estimate Std. Error Lower CI Upper CI
1      1.0       0.86  -0.6856    2.686
2      0.5       0.64  -0.7544    1.754
3     -2.0       0.32  -2.6272   -1.373

Test:
IBGA

p-value:
0.2299

Power:
0.3088

Alpha:
0.05

> plot(test9)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qualint.Rnw’ using Sweave
Loading required package: survival
Loading required package: ggplot2

Error: processing vignette 'qualint.Rnw' failed with diagnostics:
 chunk 4 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘qualint.Rnw’

--- re-building ‘qualval.Rnw’ using Sweave
Loading required package: survival
Loading required package: ggplot2

Error: processing vignette 'qualval.Rnw' failed with diagnostics:
 chunk 3 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘qualval.Rnw’

SUMMARY: processing the following files failed:
  ‘qualint.Rnw’ ‘qualval.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    nasa

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 111-120 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addSpecialProteins
> ### Title: add special labels
> ### Aliases: addSpecialProteins
> 
> ### ** Examples
> 
> 
> foldchange <- rnorm(1000)
> pvals <-rexp(1000)
> names <- sample(colors(),1000,replace=TRUE)
> 
> dataX <- data.frame(
+   q.mod = pvals,
+   log2FC = foldchange,
+   names = names
+ )
> library(rlang)
> foldchange = "log2FC"
> p <- volcano2GB(dataX, pthresh=0.1, log2FCThresh=0.5 , main='test',
+                 repel.segment.size=0.3,
+                 repel.text.size=2)
> special <- sample(colors(),5)
> p <- addSpecialProteins(p, dataX, special)
> p
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning: Removed 993 rows containing missing values (geom_text_repel).
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘quanteda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textplot_keyness
> ### Title: Plot word keyness
> ### Aliases: textplot_keyness
> ### Keywords: textplot
> 
> ### ** Examples
> 
> # compare Trump speeches to other Presidents by chi^2
> dfmat1 <- data_corpus_inaugural %>%
+      corpus_subset(Year > 1980) %>%
+      dfm(groups = "President", remove = stopwords("english"), remove_punct = TRUE)
> tstat1 <- textstat_keyness(dfmat1, target = "Trump")
> textplot_keyness(tstat1, margin = 0.2, n = 10)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
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 158-166 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Release.Rmd’ using rmarkdown
--- finished re-building ‘Release.Rmd’

--- re-building ‘Use_case.Rmd’ using rmarkdown
Quitting from lines 119-120 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Use_case.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.queue_list
> ### Title: ggplot2 method for output from queueing model
> ### Aliases: plot.queue_list
> 
> ### ** Examples
> 
> if(require(ggplot2, quietly = TRUE)){
+ 
+ n_customers <- 50
+ arrival_rate <- 1.8
+ service_rate <- 1
+ arrivals <- cumsum(rexp(n_customers, arrival_rate))
+ service <- rexp(n_customers, service_rate)
+ queue_obj <- queue_step(arrivals, service, servers = 2)
+ plot(queue_obj)
+ 
+ }
[[1]]
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘iii-plotting.Rmd’ using rmarkdown

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: sp

Attaching package: 'raster'

The following object is masked from 'package:data.table':

    shift

Quitting from lines 128-134 (iii-plotting.Rmd) 
Error: processing vignette 'iii-plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘iii-plotting.Rmd’

SUMMARY: processing the following file failed:
  ‘iii-plotting.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cum_normal_fun
> ### Title: Cumulative normal function
> ### Aliases: cum_normal_fun
> 
> ### ** Examples
> 
> xseq <- seq(0,4,.01)
> yseq <- cum_normal_fun(xseq, c(2, .5))
> curve <- data.frame(x = xseq, y = yseq)
> ggplot(curve, aes(x = x, y = y)) + geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘quickReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reg
> ### Title: plot the result of regression result
> ### Aliases: plot.reg plot_reg
> 
> ### ** Examples
> 
> reg_glm<-reg(data = diabetes, y = 5, factor = c(1, 3, 4), model = 'glm')
> plot(reg_glm)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickReg.Rmd’ using rmarkdown
Quitting from lines 131-162 (quickReg.Rmd) 
Error: processing vignette 'quickReg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickReg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quokar.Rmd’ using rmarkdown
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'dplyr'

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

    combine

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 62-63 (quokar.Rmd) 
Error: processing vignette 'quokar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quokar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘qwraps2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2_extract_legend
> ### Title: ggplot2 tools
> ### Aliases: ggplot2_extract_legend
> 
> ### ** Examples
> 
> # a simple plot
> my_plot <- 
+   ggplot2::ggplot(mtcars) + 
+   ggplot2::aes(x = wt, y = mpg, color = wt, shape = factor(cyl)) + 
+   ggplot2::geom_point()
> 
> my_plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Loading required package: stats4

Attaching package: 'bbmle'

The following object is masked from 'package:R2admb':

    stdEr

Quitting from lines 153-164 (R2admb.Rnw) 
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘r2glmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.R2
> ### Title: Visualize standardized effect sizes and model R squared
> ### Aliases: plot.R2
> 
> ### ** Examples
> 
> library(nlme)
> library(r2glmm)
> 
> data(Orthodont)
> 
> # Linear mixed model
> lmemod = lme(distance ~ age*Sex, random = ~1|Subject, data = Orthodont)
> 
> r2 = r2beta(model=lmemod,partial=TRUE,method='sgv')
Warning in model.matrix.default(~b$groups[[n.levels - i + 1]] - 1, contrasts.arg = c("contr.treatment",  :
  non-list contrasts argument ignored
> 
> plot(x=r2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Running examples in ‘r4lineups-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_roc
> ### Title: Compute and plot ROC curve for lineup accuracy ~ confidence
> ### Aliases: make_roc
> 
> ### ** Examples
> 
> #Data:
> data(mickwick)
> 
> #Call:
> make_roc(mickwick)
Warning in roc.default(response, m[[predictors]], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Warning in roc.default(response, m[[predictors]], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 398-400 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.clt
> ### Title: Plot method for the Central Limit Theorem simulation
> ### Aliases: plot.clt
> 
> ### ** Examples
> 
> clt("Uniform", 100, 100, unif_min = 10, unif_max = 20) %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: %>% ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pivotr
> ### Title: Plot method for the pivotr function
> ### Aliases: plot.pivotr
> 
> ### ** Examples
> 
> pivotr(diamonds, cvars = "cut") %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.design-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sample_size_comp
> ### Title: Plot method for the sample_size_comp function
> ### Aliases: plot.sample_size_comp
> 
> ### ** Examples
> 
> sample_size_comp(
+   type = "proportion", p1 = 0.1, p2 = 0.15,
+   conf_lev = 0.95, power = 0.8
+ ) %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.model-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.confusion
> ### Title: Plot method for the confusion matrix
> ### Aliases: plot.confusion
> 
> ### ** Examples
> 
> data.frame(buy = dvd$buy, pred1 = runif(20000), pred2 = ifelse(dvd$buy == "yes", 1, 0)) %>%
+   confusion(c("pred1", "pred2"), "buy") %>%
+   plot()
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘radiant.multivariate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.conjoint
> ### Title: Plot method for the conjoint function
> ### Aliases: plot.conjoint
> 
> ### ** Examples
> 
> result <- conjoint(mp3, rvar = "Rating", evar = "Memory:Shape")
> plot(result, scale_plot = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot -> plot.conjoint -> %>% -> eval -> eval -> sshhr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘programming.Rmd’ using rmarkdown
Quitting from lines 39-44 (programming.Rmd) 
Error: processing vignette 'programming.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘programming.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘rags2ridges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edgeHeat
> ### Title: Visualize (precision) matrix as a heatmap
> ### Aliases: edgeHeat
> 
> ### ** Examples
> 
> ## Obtain some (high-dimensional) data
> p = 25
> n = 10
> set.seed(333)
> X = matrix(rnorm(n*p), nrow = n, ncol = p)
> colnames(X)[1:25] = letters[1:25]
> Cx <- covML(X)
> 
> ## Obtain regularized precision matrix
> P <- ridgeP(Cx, lambda = 10, type = "Alt")
> 
> ## Obtain sparsified partial correlation matrix
> PC0 <- sparsify(P, threshold = "localFDR", FDRcut = .8)$sparseParCor
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr
Step 5... prepare for plotting

- Retained elements:  11 
- Corresponding to 3.67 % of possible edges 
 
> 
> ## Visualize sparsified partial correlation matrix as heatmap
> edgeHeat(PC0)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ragt2ridges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sparsifyVAR2
> ### Title: Function that determines the support of autoregression
> ###   parameters of the VAR(2) model.
> ### Aliases: sparsifyVAR2
> 
> ### ** Examples
> 
> # set dimensions (p=covariates, n=individuals, T=time points)
> p <- 3; n <- 12; T <- 10
> 
> # set model parameters
> SigmaE <- diag(p)/4
> A1 <- -createA(p, "clique", nCliques=1, nonzeroA=0.1)
> A2 <- t(createA(p, "chain", nBands=1, nonzeroA=0.1))
> 
> # generate data
> Y <- dataVAR2(n, T, A1, A2, SigmaE)
> 
> # fit VAR(1) model
> VAR2hat <- ridgeVAR2(Y, 1, 1, 1)
> 
> # obtain support of adjacancy matrix
> A1nullornot <- matrix(0, p, p)
> A1nullornot[sparsifyVAR2(VAR2hat$A1, VAR2hat$A2, solve(VAR1hat$P), 
+                          threshold="top", top=c(3,3))$nonzerosA1] <- 1
-> Retained elements of A1:  3 
-> Corresponding to 33.33 % of possible A1 elements 
-> Retained elements of A2:  3 
-> Corresponding to 33.33 % of possible A2 elements 
> 
> ## plot non-null structure of A1 
> edgeHeat(A1nullornot)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Warning: Removed 39 rows containing missing values (geom_path).
Quitting from lines 408-418 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘raincpc_demo.Rmd’ using knitr
Loading required package: sp

Attaching package: 'raster'

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

    distance

Quitting from lines 103-117 (raincpc_demo.Rmd) 
Error: processing vignette 'raincpc_demo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘raincpc_demo.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OTU.recap
> ### Title: Summarize OTU
> ### Aliases: OTU.recap
> ### Keywords: math
> 
> ### ** Examples
> 
> data(ITS1, ITS2)
> ranks <- c("p", "c", "o", "f", "g")
> df <- OTU.recap(data=list(ITS1=ITS1, ITS2=ITS2), ranks=ranks)
Using ind as id variables
Using ind as id variables
Warning in brewer.pal(len, brewer.pal) :
  n too large, allowed maximum for palette Pastel1 is 9
Returning the palette you asked for with that many colors

Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: OTU.recap ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘randomForestExplainer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_importance_ggpairs
> ### Title: Plot importance measures with ggpairs
> ### Aliases: plot_importance_ggpairs
> 
> ### ** Examples
> 
> forest <- randomForest::randomForest(Species ~ ., data = iris, localImp = TRUE, ntree = 200)
> frame <- measure_importance(forest, measures = c("mean_min_depth", "times_a_root"))
Warning: Factor `split var` contains implicit NA, consider using `forcats::fct_explicit_na`
> plot_importance_ggpairs(frame, measures = c("mean_min_depth", "times_a_root"))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomForestExplainer.Rmd’ using rmarkdown
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 68-70 (randomForestExplainer.Rmd) 
Error: processing vignette 'randomForestExplainer.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘randomForestExplainer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rnw’ using knitr
Warning in remind_sweave(if (in.file) input, sweave_lines) :
  It seems you are using the Sweave-specific syntax in line(s) 766; you may need Sweave2knitr("article.Rnw") to convert it to knitr
Loading required package: ggplot2
Loading required package: plotrix
Quitting from lines 927-929 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘article.Rnw’

--- re-building ‘comparison-example.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: plotrix
Quitting from lines 153-154 (comparison-example.Rnw) 
Error: processing vignette 'comparison-example.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘comparison-example.Rnw’

--- re-building ‘desirability-example.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: plotrix
--- finished re-building ‘desirability-example.Rnw’

--- re-building ‘randomizeR-refCard.Rnw’ using knitr
--- finished re-building ‘randomizeR-refCard.Rnw’

SUMMARY: processing the following files failed:
  ‘article.Rnw’ ‘comparison-example.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot,rmap.frame,missing-method
> ### Title: Plot a rmap.frame
> ### Aliases: plot,rmap.frame,missing-method
> 
> ### ** Examples
> 
> require(rangeMapper)
> breding_ranges = rgdal::readOGR(system.file(package = "rangeMapper",
+      "extdata", "wrens", "vector_combined"), "wrens", verbose = FALSE)[1:70, ]
> data(wrens)
> d = subset(wrens, select = c('sci_name', 'body_mass', 'clutch_size') )
> con = ramp("wrens.sqlite", gridSize = 4, spdf = breding_ranges, biotab = d, ID = "sci_name",
+             FUN = "median", overwrite = TRUE)
New session 2019-03-29 23:24:55
PROJECT: wrens.sqlite 
DIRECTORY: /tmp/RtmpwzliJu
Grid size set to 4 map units.
Canvas uploaded.
Writing overlay output to project...
70 out of 70 ranges updated; Elapsed time: 0 mins
Table biotab saved as a  BIO_ table
+______________+
class            rangeMap
Project_location /tmp/RtmpwzliJu/wrens.sqlite
Proj4            +proj=longlat +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +no_defs
CellSize         4
Extent           xmin=-126.1848,xmax=-34.79333,ymin=-55.72056,ymax=59.32195
BIO_tables       biotab
MAP_tables       species_richness;median_body_mass;median_clutch_size
METADATA_RANGES  
+______________+
> m = rangeMap.fetch(con, c('median_body_mass', 'median_clutch_size'), spatial = FALSE)
> plot(m, ncol = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rangemodelR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rangemod2d
> ### Title: Range Cohesion Models for Spatial Polygon Grids
> ### Aliases: rangemod2d
> 
> ### ** Examples
> 
> if(require(rgdal)&&require(maptools)&&require(rgeos)&&require(ggplot2)){
+ data(shp)
+ data(neigh_ob)
+ data(spmat)
+ mod.out <- rangemod2d(spmat,shp,"ID",nb = neigh_ob,rsize = "observed",
+                        var = NULL,reps = 5)
+ shp.out <- mod.out$out.shp
+ shp.out.df <- shp.out@data
+ shp.out.fort <- fortify(shp.out,region = "ID")
+ seq <- match(shp.out.fort$id,shp.out.df$ID)
+ shp.out.gg <- data.frame(shp.out.fort,shp.out.df[seq,])
+ ggplot(shp.out.gg)+
+   geom_map(map=shp.out.gg,aes_string(map_id="id",
+                                      fill = "mod.rich"))+
+   geom_path(aes(x = long,y = lat,group = group),colour = "white")+
+   coord_equal() + theme_bw()+
+   scale_fill_continuous(low = "white",high = "black")
+ }
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Loading required package: maptools
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.4-2, (SVN revision 581)
 GEOS runtime version: 3.7.1-CAPI-1.11.1 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘raptr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: space.plot
> ### Title: Plot space
> ### Aliases: space.plot space.plot.RapData space.plot.RapUnsolved
> ###   space.plot.RapSolved
> 
> ### ** Examples
> 
> # load RapSolved objects
> data(sim_ru, sim_rs)
> 
> # plot first species in first attribute space
> space.plot(sim_ru, 1, 1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
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-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RDperm.Rnw’ using knitr
Loading required package: RATest
Loading required package: ggplot2
Loading required package: gridExtra
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Quitting from lines 616-651 (RDperm.Rnw) 
Error: processing vignette 'RDperm.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RDperm.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsr
> ### Title: Rating scale reduction
> ### Aliases: rsr
> 
> ### ** Examples
> 
> #creating the matrix of attributes and the decision vector
> #must be as.numeric()
> data(aSAH)
> attach(aSAH)
> is.numeric(aSAH)
[1] FALSE
> 
> attribute <-data.frame(as.numeric(gender), 
+ as.numeric(age), as.numeric(wfns), as.numeric(s100b), as.numeric(ndka))
> colnames(attribute) <-c("a1", "a2", "a3", "a4", "a5")
> decision <-as.numeric(outcome)
> 
> #rating scale reduction procedure
> rsred <-rsr(attribute, decision, plotRSR=TRUE)
> rsred
$rsr.auc
[1] 0.8236789 0.8241870

$rsr.label
[1] "a3" "a4"

$summary
   AUC one variable AUC running total
a3        0.8236789         0.8236789
a4        0.7313686         0.8241870

[[4]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RBesT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: forest_plot
> ### Title: Forest Plot
> ### Aliases: forest_plot
> 
> ### ** Examples
> 
> # we consider the example AS MAP analysis
> example(AS)

AS> set.seed(34563)

AS> map_AS <- gMAP(cbind(r, n-r) ~ 1 | study,
AS+                family=binomial,
AS+                data=AS,
AS+                tau.dist="HalfNormal", tau.prior=1,
AS+                beta.prior=2,
AS+                ## ensure fast example runtime
AS+                thin=1, chains=1)
Assuming default prior location   for beta: 0
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
> 
> # default forest plot for a gMAP analysis
> forest_plot(map_AS)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rbin_equal_length
> ### Title: Equal length binning
> ### Aliases: rbin_equal_length plot.rbin_equal_length
> 
> ### ** Examples
> 
> bins <- rbin_equal_length(mbank, y, age, 10)
> bins
Binning Summary
---------------------------------
Method               Equal Length 
Response             y 
Predictor            age 
Bins                 10 
Count                4521 
Goods                517 
Bads                 4004 
Entropy              0.5 
Information Value    0.17 


# A tibble: 10 x 7
   cut_point bin_count  good   bad     woe       iv entropy
   <chr>         <int> <int> <int>   <dbl>    <dbl>   <dbl>
 1 < 24.6           85    24    61 -1.11   0.0347     0.859
 2 < 31.2          822   106   716 -0.137  0.00358    0.555
 3 < 37.8         1133   115  1018  0.134  0.00425    0.474
 4 < 44.4          943    82   861  0.304  0.0172     0.426
 5 < 51            623    52   571  0.349  0.0147     0.414
 6 < 57.6          612    66   546  0.0660 0.000574   0.493
 7 < 64.2          229    43   186 -0.582  0.0214     0.697
 8 < 70.8           34    12    22 -1.44   0.0255     0.937
 9 < 77.4           25    13    12 -2.13   0.0471     0.999
10 >= 77.4          15     4    11 -1.04   0.00517    0.837
> 
> # plot
> plot(bins)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 59-61 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Running examples in ‘rcartocolor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_carto_c
> ### Title: CARTO color scales
> ### Aliases: scale_color_carto_c scale_color_carto_d scale_colour_carto_c
> ###   scale_colour_carto_d scale_fill_carto_c scale_fill_carto_d
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ggplot(msleep, aes(vore, sleep_total, fill = vore)) +
+         geom_boxplot() +
+         scale_fill_carto_d(palette = 6, direction = -1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rchess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggchessboard
> ### Title: Plot a fen representation chessboard via ggplot2
> ### Aliases: ggchessboard
> 
> ### ** Examples
> 
> ggchessboard()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ec_climate.Rmd’ using rmarkdown
Warning: Removed 14 rows containing missing values (geom_path).
Quitting from lines 96-107 (ec_climate.Rmd) 
Error: processing vignette 'ec_climate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ec_climate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fuzzyrcmdrplugin.Rmd’ using rmarkdown
Quitting from lines 72-73 (fuzzyrcmdrplugin.Rmd) 
Error: processing vignette 'fuzzyrcmdrplugin.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fuzzyrcmdrplugin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘RcmdrPlugin.KMggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stepribbon
> ### Title: Step ribbon plots.
> ### Aliases: GeomStepribbon geom_stepribbon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> huron <- data.frame(year = 1875:1972, level = as.vector(LakeHuron))
> h <- ggplot(huron, aes(year))
> h + geom_stepribbon(aes(ymin = level - 1, ymax = level + 1), fill = "grey70") +
+     geom_step(aes(y = level))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extrafont.Rmd’ using rmarkdown
--- finished re-building ‘extrafont.Rmd’

--- re-building ‘geom-stepribbon.Rmd’ using rmarkdown
Quitting from lines 38-84 (geom-stepribbon.Rmd) 
Error: processing vignette 'geom-stepribbon.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geom-stepribbon.Rmd’

--- re-building ‘plot-km-requirement.Rmd’ using rmarkdown
--- finished re-building ‘plot-km-requirement.Rmd’

SUMMARY: processing the following file failed:
  ‘geom-stepribbon.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘RCMIP5-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: worldPlot
> ### Title: Plot global data
> ### Aliases: worldPlot
> 
> ### ** Examples
> 
> d <- cmip5data(1970:1975)   # sample data
> worldPlot(d)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppDynProg.Rmd’ using rmarkdown
Quitting from lines 63-84 (RcppDynProg.Rmd) 
Error: processing vignette 'RcppDynProg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RcppDynProg.Rmd’

--- re-building ‘Segmentation.Rmd’ using rmarkdown
Quitting from lines 16-41 (Segmentation.Rmd) 
Error: processing vignette 'Segmentation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Segmentation.Rmd’

--- re-building ‘SegmentationL.Rmd’ using rmarkdown
Quitting from lines 16-47 (SegmentationL.Rmd) 
Error: processing vignette 'SegmentationL.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SegmentationL.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppDynProg.Rmd’ ‘Segmentation.Rmd’ ‘SegmentationL.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdbnomics.Rmd’ using rmarkdown
Quitting from lines 182-185 (rdbnomics.Rmd) 
Error: processing vignette 'rdbnomics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rdbnomics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rdplotdensity
> ### Title: Density Plot
> ### Aliases: rdplotdensity
> 
> ### ** Examples
> 
> # density being discontinuous
> set.seed(42)
> x <- rnorm(2000, mean = -0.5); x[x>0] <- x[x>0] * 2
> rdd <- rddensity(X = x)
> plot <- rdplotdensity(rdd, x, plotRange = c(-2, 2), plotN = 25)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rdplotdensity ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rddtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPlacebo
> ### Title: Draw a (density) plot of placebo tests
> ### Aliases: computePlacebo plotPlacebo plotPlacebo.rdd_reg plotPlaceboDens
> ###   plotPlaceboDens.rdd_reg
> 
> ### ** Examples
> 
> data(house)
> house_rdd <- rdd_data(y=house$y, x=house$x, cutpoint=0)
> reg_nonpara <- rdd_reg_np(rdd_object=house_rdd)
> plotPlacebo(reg_nonpara)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotPlacebo ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘morocco.Rmd’ using rmarkdown
Quitting from lines 99-100 (morocco.Rmd) 
Error: processing vignette 'morocco.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘morocco.Rmd’

--- re-building ‘rddtools.Rmd’ using rmarkdown
Quitting from lines 69-70 (rddtools.Rmd) 
Error: processing vignette 'rddtools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rddtools.Rmd’

SUMMARY: processing the following files failed:
  ‘morocco.Rmd’ ‘rddtools.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertRDI
> ### Title: Convert RDI measures
> ### Aliases: convertRDI
> 
> ### ** Examples
> 
> 
> #create genes
> genes = sample(letters, 10000, replace=TRUE)
> #create sequence annotations
> seqAnnot = data.frame(donor = sample(1:4, 10000, replace=TRUE))
> #calculate RDI
> d = rdi(genes, seqAnnot)
> 
> ##convert RDI to actual 'lfc' estimates and compare
> dtrue = convertRDI(d)$pred
> plot(d, dtrue)
> 
> ##look at SD ranges around lfc estimates
> dtrue = convertRDI(d, calcSD=TRUE)
> 
> ##plot using ggplot2
> library(ggplot2)
> x = as.numeric(d)
> y = as.numeric(dtrue$pred)
> sd = as.numeric(dtrue$sd)
> qplot(x,y)+geom_errorbar(aes(x=x, ymin=y-sd, ymax=y+sd))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rdiversity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_diversity
> ### Title: Plot diversity
> ### Aliases: plot_diversity
> 
> ### ** Examples
> 
> # Define metacommunity
> pop <- data.frame(a = c(1,3), b = c(1,1))
> row.names(pop) <- paste0("sp", 1:2)
> pop <- pop/sum(pop)
> meta <- metacommunity(pop)
> 
> # Calculate subcommunity beta diversity (takes the relative entropy)
> b <- raw_beta(meta)
> res <- subdiv(b, 0:2)
> plot_diversity(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CreateRDML.Rmd’ using rmarkdown
Loading required package: robustbase
Warning: Removed 29 rows containing missing values (geom_point).
Quitting from lines 56-63 (CreateRDML.Rmd) 
Error: processing vignette 'CreateRDML.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CreateRDML.Rmd’

--- re-building ‘RDML.Rmd’ using rmarkdown
knitr hook "anchor" is now available
Quitting from lines 246-259 (RDML.Rmd) 
Error: processing vignette 'RDML.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RDML.Rmd’

--- re-building ‘usingRDML_with_other_R_packages.Rmd’ using rmarkdown
Quitting from lines 96-107 (usingRDML_with_other_R_packages.Rmd) 
Error: processing vignette 'usingRDML_with_other_R_packages.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usingRDML_with_other_R_packages.Rmd’

SUMMARY: processing the following files failed:
  ‘CreateRDML.Rmd’ ‘RDML.Rmd’ ‘usingRDML_with_other_R_packages.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/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
Quitting from lines 172-174 (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:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Running examples in ‘RDS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bottleneck.plot
> ### Title: Bottleneck Plot
> ### Aliases: bottleneck.plot
> 
> ### ** Examples
> 
> data(fauxmadrona)
> bottleneck.plot(fauxmadrona,"disease")
[1] "194"
[1] "298"
[1] "164"
[1] "617"
[1] "586"
[1] "322"
[1] "729"
[1] "925"
[1] "992"
[1] "356"
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘realestateDK.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 82-86 (realestateDK.Rmd) 
Error: processing vignette 'realestateDK.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘realestateDK.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Custom_Steps.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'recipes'

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

    step

Quitting from lines 49-54 (Custom_Steps.Rmd) 
Error: processing vignette 'Custom_Steps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Custom_Steps.Rmd’

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

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

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

--- re-building ‘Selecting_Variables.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'recipes'

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

    step

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

--- re-building ‘Simple_Example.Rmd’ using rmarkdown
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'recipes'

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

    step

Loading required package: tidyr
--- finished re-building ‘Simple_Example.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcf
> ### Title: Mean Cumulative Function (MCF)
> ### Aliases: mcf mcf,formula-method mcf,rateReg-method
> 
> ### ** Examples
> 
> library(reda)
> 
> ### sample MCF
> ## Example 1. valve-seat data
> ## the default variance estimates by Lawless and Nadeau (1995) method
> valveMcf0 <- mcf(Survr(ID, Days, No.) ~ 1, data = valveSeats)
> plot(valveMcf0, conf.int = TRUE, mark.time = TRUE, addOrigin = TRUE) +
+     ggplot2::xlab("Days") + ggplot2::theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘reda-intro.Rmd’ using rmarkdown
Quitting from lines 122-128 (reda-intro.Rmd) 
Error: processing vignette 'reda-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘reda-intro.Rmd’

--- re-building ‘reda-simulate.Rmd’ using rmarkdown
--- finished re-building ‘reda-simulate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 27-67 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_model
> ### Title: Graph interactions for fitted models.
> ### Aliases: graph_model graph_model.lm graph_model.aov graph_model.glm
> ###   graph_model.lme graph_model.merMod
> 
> ### ** Examples
> 
> # iris data
> model <- lm(Sepal.Width ~ Sepal.Length * Species, data=iris)
> graph_model_q(model, y='Sepal.Width', x='Sepal.Length', lines='Species')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘regrrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_effect
> ### Title: plotting the marginal effect of X on Y, with or without one or
> ###   multiple interaction terms
> ### Aliases: plot_effect
> 
> ### ** Examples
> 
> data(mtcars)
> m1 <- lm(mpg ~ vs + carb + hp + wt + wt * hp , data = mtcars)
> plot_effect(reg.coef = summary(m1)$coefficients, 
+                  data = mtcars, model = m1, 
+                  x_var.name = "wt", y_var.name = "mpg", moderator.name = "hp", 
+                  confidence_interval = TRUE,  CI_Ribbon = TRUE, 
+                  xlab = "Weight", ylab = "MPG", moderator.lab = "Horsepower")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘reinsureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw
> ### Title: Claims: Plot function
> ### Aliases: draw draw,Claims-method
> 
> ### ** Examples
> 
> c <- data.frame(year = unlist(sapply(2000:2017, function(x) rep(x, rpois(1,3)))))
> c$amount <- pmax(rnorm(nrow(c), 200000, 100000), 0)
> p <- aggregate(amount ~ year, c, sum)
> claims <- claims(c, p)
> treaty_1 <- xl(ded = 100000, lim = 20000, aad = 5000,
+                aal = 200000, prm = 0.01, rns = 1)
> claims <- apply_treaty(claims, treaty_1)
> draw(claims)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rentrez_tutorial.Rmd’ using rmarkdown
Quitting from lines 155-158 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘rentrez_tutorial.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBed
> ### Title: A function to boxplot 'score' column of a BED dataframe, per
> ###   unique chromosome name in the <e2><80><98>chrom<e2><80><99> column.
> ###   The resulting plot also highlights outliers based on the inter
> ###   quartile range (IQR). The genome wide median is plotted as a pink
> ###   line through the boxplots.
> ### Aliases: plotBed
> ### Keywords: BED bioinformatics boxplot genomics
> 
> ### ** Examples
> 
> plotBed(W303_S)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DependencySorting.Rmd’ using rmarkdown
--- finished re-building ‘DependencySorting.Rmd’

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

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

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: wrapr

Attaching package: 'wrapr'

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

    coalesce

Quitting from lines 111-115 (letExample.Rmd) 
Error: processing vignette 'letExample.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘letExample.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘replyr.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxplotAndDensityCurveOnHistogram
> ### Title: boxplotAndDensityCurveOnHistogram
> ### Aliases: boxplotAndDensityCurveOnHistogram
> 
> ### ** Examples
> 
> library(ggplot2)
> library(grid)
> library(gridExtra)
> boxplotAndDensityCurveOnHistogram(Madeyski15EISEJ.PropProjects, "STUD", 0, 100)
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 2 rows containing missing values (geom_bar).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: boxplotAndDensityCurveOnHistogram ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘reReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reReg
> ### Title: Plotting Baseline Cumulative Rate Function and Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(readmission, package = "frailtypack")
> fit <- reReg(reSurv(t.stop, id, event, death) ~ sex + chemo,
+              data = subset(readmission, id < 50))
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
> plot(fit)
Baseline cumulative hazard function is not available for method = cox.LWYY.
Only the baseline cumulative rate function is plotted.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rERR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: f_plot_linERR_ef
> ### Title: plot likelihood function from ef
> ### Aliases: f_plot_linERR_ef
> 
> ### ** Examples
> 
> # set the formulas for the models
> formula1  <- Surv(entry_age,exit_age,outcome) ~ lin(dose_cum) + strata(sex)
> 
> # fit the model
> fit1 <- f_fit_linERR_ef(formula1,data=cohort_ef,id_name="id",dose_name="dose",
+                         time_name="age",covars_names=c("sex"),lag=2,exclusion_done=TRUE)
>                         
> # plot the partial loglikelihood function
> f_plot_linERR_ef(fit1,formula1,data=cohort_ef,id_name="id",dose_name="dose",
+                         time_name="age",covars_names=c("sex"),lag=2,exclusion_done=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘retrodesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim_plot
> ### Title: sim_plot: visualize type S/M errors
> ### Aliases: sim_plot
> 
> ### ** Examples
> 
> sim_plot(1,3.28)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_To_retrodesign.Rmd’ using rmarkdown
Quitting from lines 91-92 (Intro_To_retrodesign.Rmd) 
Error: processing vignette 'Intro_To_retrodesign.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_To_retrodesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using knitr
Loading required package: rivr
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Quitting from lines 73-74 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘revdbayes-a-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-a-vignette.Rmd’

--- re-building ‘revdbayes-b-using-rcpp-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-b-using-rcpp-vignette.Rmd’

--- re-building ‘revdbayes-c-predictive-vignette.Rmd’ using rmarkdown
Quitting from lines 98-101 (revdbayes-c-predictive-vignette.Rmd) 
Error: processing vignette 'revdbayes-c-predictive-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘revdbayes-c-predictive-vignette.Rmd’

--- re-building ‘revdbayes-d-kgaps-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-d-kgaps-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘revdbayes-c-predictive-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘log_parsing.Rmd’ using rmarkdown
Read 1000 items
Quitting from lines 69-71 (log_parsing.Rmd) 
Error: processing vignette 'log_parsing.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘log_parsing.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rfm_bar_chart
> ### Title: RFM bar chart
> ### Aliases: rfm_bar_chart
> 
> ### ** Examples
> 
> # using transaction data
> analysis_date <- lubridate::as_date('2006-12-31', tz = 'UTC')
> rfm_order <- rfm_table_order(rfm_data_orders, customer_id, order_date,
+ revenue, analysis_date)
> 
> # bar chart
> rfm_bar_chart(rfm_order)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rfm_bar_chart ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown

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 116-117 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown

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 113-114 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impHeatmap
> ### Title: Importance Heatmap
> ### Aliases: impHeatmap
> 
> ### ** Examples
> 
> data(mtcars)
> 
> # A randomForest model
> rf <- randomForest(factor(am) ~ ., mtcars, importance = TRUE)
> importance(rf)
              0          1 MeanDecreaseAccuracy MeanDecreaseGini
mpg   3.6085439  4.8299920            5.1570120        1.0513643
cyl   1.1006672  1.8752027            2.0963503        0.2128961
disp  5.2145802  8.0631572            8.4476655        1.8481357
hp    1.9174919  4.9738587            5.0371940        0.8768533
drat  5.5743157  9.0046005            9.0753230        2.0552791
wt   12.6460573 16.7371824           17.2904661        3.8012383
qsec  5.9572770  3.7329653            5.4690146        1.3975243
vs    3.6146152  0.5608144            2.9643967        0.1430843
gear  9.4788534 13.9098472           13.9703043        3.1261030
carb  0.3580251 -0.9342927           -0.5446649        0.4398967
> impHeatmap(rf, xlab = "Transmission", ylab = "Predictor")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: impHeatmap ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_RGCCA.Rmd’ using rmarkdown
Quitting from lines 737-753 (vignette_RGCCA.Rmd) 
Error: processing vignette 'vignette_RGCCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_RGCCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
ggtree v1.15.6  For help: https://guangchuangyu.github.io/software/ggtree

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628


Loading required package: ape

Attaching package: 'ape'

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

    rotate

Loading required package: maps

Attaching package: 'phytools'

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

    read.newick

Warning in load_fasta(fasta.file.name) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Quitting from lines 106-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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-patched-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Running examples in ‘ri2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conduct_ri
> ### Title: Conduct Randomization Inference
> ### Aliases: conduct_ri
> 
> ### ** Examples
> 
> 
> # Data from Gerber and Green Table 2.2
> 
> 
> # Randomization Inference for the Average Treatment Effect
> 
> table_2.2 <-
+     data.frame(d = c(1, 0, 0, 0, 0, 0, 1),
+                y = c(15, 15, 20, 20, 10, 15, 30))
> 
> ## Declare randomization procedure
> declaration <- declare_ra(N = 7, m = 2)
> 
> ## Conduct Randomization Inference
> out <- conduct_ri(y ~ d,
+                       declaration = declaration,
+                       assignment = "d",
+                       sharp_hypothesis = 0,
+                       data = table_2.2)
> 
> summary(out)
  term estimate two_tailed_p_value
1    d      6.5          0.3809524
> plot(out)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ri2_vignette.Rmd’ using rmarkdown
Quitting from lines 42-57 (ri2_vignette.Rmd) 
Error: processing vignette 'ri2_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ri2_vignette.Rmd’

--- re-building ‘ri2_vs_ri.Rmd’ using rmarkdown
--- finished re-building ‘ri2_vs_ri.Rmd’

SUMMARY: processing the following file failed:
  ‘ri2_vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_image
> ### Title: Image color scales
> ### Aliases: scale_color_image scale_colour_image scale_fill_image
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # ripped from the pages of ggplot2
> your_image <- jpeg::readJPEG(system.file("img", "Rlogo.jpg", package="jpeg"))
> display_image(your_image)
> 
> #Discrete scale example
> p <- ggplot(mtcars, aes(wt, mpg))
> p + geom_point(size=4, aes(colour = factor(cyl))) +
+     scale_color_image(image = your_image) +
+     theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rinatVignette.Rmd’ using rmarkdown
Quitting from lines 180-188 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rinatVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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:2352:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2382:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2428:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2500:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2518:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  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-patched-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Running examples in ‘rise-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rise
> ### Title: RISE Analysis
> ### Aliases: rise
> 
> ### ** Examples
> 
> library(ggplot2)
> rise(sample_df, visual = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.predictCSC
> ### Title: Plot Predictions From a Cause-specific Cox Proportional Hazard
> ###   Regression
> ### Aliases: autoplot.predictCSC
> 
> ### ** Examples
> 
> library(survival)
> library(rms)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula

Attaching package: ‘Hmisc’

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

    format.pval, units

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

> 
> #### simulate data ####
> set.seed(10)
> d <- sampleData(1e2, outcome = "competing.risks")
> 
> #### CSC model ####
> m.CSC <- CSC(Hist(time,event)~ X1 + X2 + X6, data = d)
> 
> pred.CSC <- predict(m.CSC, newdata = d[1:2,], time = 1:5, cause = 1)#'
> autoplot(pred.CSC)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: autoplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘publication-reproduction.Rmd’ using rmarkdown
--- finished re-building ‘publication-reproduction.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Quitting from lines 100-104 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

--- re-building ‘technical-vignette.Rmd’ using rmarkdown
--- finished re-building ‘technical-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estEllipse
> ### Title: Estimate Bivariate Normal Ellipse Isotope Niche
> ### Aliases: estEllipse
> 
> ### ** Examples
> 
> library(rKIN)
> data("rodents")
> #estimate niche overlap between 2 species using bivariate ellipse
> test.elp<- estEllipse(data=rodents, x="Ave_C", y="Ave_N", group="Species",
+                      levels=c(50, 75, 95))
> #determine polygon overlap for all polygons
> plotKIN(test.elp, scaler=2, title="Ellipse Estimates", xlab="Ave_C", ylab="Ave_N")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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-patched-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Running examples in ‘Rmagic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.magic
> ### Title: Convert a MAGIC object to a data.frame for ggplot
> ### Aliases: ggplot.magic
> 
> ### ** Examples
> 
> if (reticulate::py_module_available("magic") && require(ggplot2)) {
+ 
+ data(magic_testdata)
+ data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))
+ ggplot(data_magic, aes(VIM, CDH1, colour=ZEB1)) +
+   geom_point()
+ 
+ }
Loading required package: ggplot2
Error in py_get_attr_impl(x, name, silent) : 
  AttributeError: module 'magic' has no attribute 'MAGIC'
Calls: magic ... py_get_attr_or_item -> py_get_attr -> py_get_attr_impl
Execution halted
Found the following significant warnings:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RMariaDB.Rcheck/00install.out’ for details.
Running examples in ‘rmcorr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rmc
> ### Title: Plot the repeated measures correlation coefficient.
> ### Aliases: plot.rmc
> 
> ### ** Examples
> 
> ## Bland Altman 1995 data
> my.rmc <- rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH, dataset = bland1995)
Warning in rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH,  :
  'Subject' coerced into a factor
> plot(my.rmc, overall = TRUE)
> 
> #using ggplot instead
> ggplot2::ggplot(bland1995, ggplot2::aes(x = PacO2, y = pH, group = factor(Subject),
+       color = factor(Subject))) +
+       ggplot2::geom_point(ggplot2::aes(colour = factor(Subject))) +
+       ggplot2::geom_line(ggplot2::aes(y = my.rmc$model$fitted.values), linetype = 1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RMCriteria-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RPrometheeI
> ### Title: RPrometheeI
> ### Aliases: RPrometheeI RPrometheeI,RPrometheeArguments-method
> ### Keywords: decision-analysis decision-method mcda promethee
> 
> ### ** Examples
> 
> library(RMCriteria)
> ## Create objects for each argument
> data <-matrix(c(5.2, -3.5,
+                 4.3, -1.2,
+                 6.7, -2.0), byrow = TRUE, ncol = 2, nrow = 3)
> 
> parms <- matrix(c(NA, NA), byrow = TRUE, ncol = 1, nrow = 2)
> vecWeights <- c(0.3, 0.7)
> vecMaximiz <- c(FALSE, TRUE)
> prefFunction <- c(0, 0)
> normalize <- FALSE
> alternatives <- c("Alt 1", "Alt 2", "Alt 3")
> 
> ## Create RPrometheeArguments object
> PromObj <- RPrometheeConstructor(datMat = data, vecWeights = vecWeights,
+ vecMaximiz = vecMaximiz, prefFunction = prefFunction,
+ parms = parms, normalize = normalize, alternatives = alternatives)
> 
> ## Run RPrometheeI
> (result <- RPrometheeI(PromObj))
Promethee I object with 3 alternatives. 
Phi Plus: 0.095 0.738 0.237 
Phi Minus: 0.710 0.000 0.360 
The alternatives are: 1 2 3> 
> ## There are two alternatives two plot a RPrometheeI object:
> plot(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rmetalog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.metalog
> ### Title: Plot of the metalog object
> ### Aliases: plot.metalog
> 
> ### ** Examples
> 
> # Load example data
> data("fishSize")
> 
> # Create a bounded metalog object
> myMetalog <- metalog(fishSize$FishSize,
+                      bounds=c(0, 60),
+                      boundedness = 'b',
+                      term_limit = 13)
> 
> plot(myMetalog)
$pdf
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rmetalog-vignette.Rmd’ using rmarkdown
Quitting from lines 70-71 (rmetalog-vignette.Rmd) 
Error: processing vignette 'rmetalog-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rmetalog-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x5595bc160108>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
Running examples in ‘rmweather-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rmw_plot_normalised
> ### Title: Function to plot the meteorologically normalised time series
> ###   after 'rmw_normalise'.
> ### Aliases: rmw_plot_normalised
> 
> ### ** Examples
> 
> 
> # Plot normalised example data
> rmw_plot_normalised(data_london_normalised)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rncl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rnmr1D.Rmd’ using knitr
Quitting from lines 213-219 (Rnmr1D.Rmd) 
Error: processing vignette 'Rnmr1D.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Rnmr1D.Rmd’

SUMMARY: processing the following file failed:
  ‘Rnmr1D.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/9s]
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] 280452 - 888626 == -608174
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RNOmni.Rmd’ using rmarkdown
Quitting from lines 40-50 (RNOmni.Rmd) 
Error: processing vignette 'RNOmni.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RNOmni.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clustCoDa
> ### Title: Cluster analysis for compositional data
> ### Aliases: clustCoDa plot.clustCoDa
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(expenditures)
> x <- expenditures
> rr <- clustCoDa(x, k=6, scale = "robust", transformation = "pivotCoord")

 *** running Mclust cluster algorithm...

 *** calculating validity measure... 

 finished
> rr2 <- clustCoDa(x, k=6, distMethod = "Aitchison", scale = "none", 
+                  transformation = "identity")

 *** running Mclust cluster algorithm...

 *** calculating validity measure... 

 finished
> rr3 <- clustCoDa(x, k=6, distMethod = "Aitchison", method = "single",
+                  transformation = "identity", scale = "none")

 *** running single cluster algorithm...

 *** calculating validity measure... 

 finished
> plot(rr)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Found the following significant warnings:
  robust.cpp:665:25: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/robfilter.Rcheck/00install.out’ for details.
Running examples in ‘robmed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fortify.test_mediation
> ### Title: Convert (robust) mediation analysis results into a data frame
> ###   for plotting
> ### Aliases: fortify.test_mediation fortify.boot_test_mediation
> ###   fortify.sobel_test_mediation fortify.list
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data("BSG2014")
> 
> # run fast and robust bootstrap test
> test <- test_mediation(BSG2014,
+                        x = "ValueDiversity",
+                        y = "TeamCommitment",
+                        m = "TaskConflict")
> 
> # data for dot plot
> dot <- fortify(test, method = "dot")
> plot_mediation(dot)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fastMcd-kmini.Rnw’ using Sweave
Loading required package: robustbase
--- finished re-building ‘fastMcd-kmini.Rnw’

--- re-building ‘lmrob_simulation.Rnw’ using Sweave
Loading required package: xtable
Loading required package: robustbase
Loading required package: ggplot2
Loading required package: GGally
Loading required package: grid
Loading required package: reshape2

Error: processing vignette 'lmrob_simulation.Rnw' failed with diagnostics:
 chunk 4 (label = fig-psi-functions) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘lmrob_simulation.Rnw’

--- re-building ‘psi_functions.Rnw’ using Sweave
Loading required package: robustbase
--- finished re-building ‘psi_functions.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coefPlot
> ### Title: Coefficient plot of a sequence of regression models
> ### Aliases: coefPlot coefPlot.grplars coefPlot.rlars coefPlot.seqModel
> ###   coefPlot.sparseLTS coefPlot.tslars coefPlot.tslarsP
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## generate data
> # example is not high-dimensional to keep computation time low
> library("mvtnorm")
> set.seed(1234)  # for reproducibility
> n <- 100  # number of observations
> p <- 25   # number of variables
> beta <- rep.int(c(1, 0), c(5, p-5))  # coefficients
> sigma <- 0.5      # controls signal-to-noise ratio
> epsilon <- 0.1    # contamination level
> Sigma <- 0.5^t(sapply(1:p, function(i, j) abs(i-j), 1:p))
> x <- rmvnorm(n, sigma=Sigma)    # predictor matrix
> e <- rnorm(n)                   # error terms
> i <- 1:ceiling(epsilon*n)       # observations to be contaminated
> e[i] <- e[i] + 5                # vertical outliers
> y <- c(x %*% beta + sigma * e)  # response
> x[i,] <- x[i,] + 5              # bad leverage points
> 
> 
> ## robust LARS
> # fit model
> fitRlars <- rlars(x, y, sMax = 10)
> # create plot
> coefPlot(fitRlars)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rlmer.Rnw’ using Sweave
Loading required package: robustlmm
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2

Error: processing vignette 'rlmer.Rnw' failed with diagnostics:
 chunk 7 (label = plotPC1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘rlmer.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotTreeHaz
> ### Title: Plotting the estimated hazard function from an rocTree object
> ### Aliases: plotTreeHaz
> 
> ### ** Examples
> 
> set.seed(1)
> dat <- simu(100, 0, 1.3)
> library(survival)
> system.time(fit <- rocTree(Surv(Time, death) ~ z1 + z2, id = id,
+ data = dat, control = list(prune = TRUE, nflds = 10)))
   user  system elapsed 
  2.388   0.039   2.476 
> plotTreeHaz(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rollply-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rollply
> ### Title: Rollply
> ### Aliases: rollply
> 
> ### ** Examples
> 
> 
> # see also vignette("rollply") for a visual introduction
> library(plyr)
> 
> # 1D example: make a trendline for a time-series
> dat <- data.frame(time     = seq.int(1000),
+                   position = cumsum(rnorm(1000,0,10)))
> 
> rollav <- rollply(dat, ~ time, wdw.size=10,
+                   summarise, position=mean(position))
> 
> plot(position ~ time, data = dat, pch = 20)
> lines(rollav, col = 'red', lwd = 3)
> 
> # 2D example
> 
> # Generate three 2D random walks
> dat <- ddply(data.frame(person = c('francois','nicolas','jacques')), 
+              ~ person,
+              summarise, time = seq.int(1000),
+                         x    = cumsum(rnorm(1000,0,1)),
+                         y    = cumsum(rnorm(1000,0,1)))
> 
> # Smoothed trajectory over ten time-steps
> rollav <- rollply(dat, ~ time | person, wdw.size = 10, grid_res = 1000,
+                   summarise, x = mean(x), y = mean(y))
> 
> if ( require(ggplot2) ) {
+   ggplot(dat, aes(x, y, color = person)) +
+     geom_point(alpha = .5, shape = '+') +
+     geom_path(data = rollav)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rollply.Rmd’ using rmarkdown
Quitting from lines 51-60 (rollply.Rmd) 
Error: processing vignette 'rollply.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rollply.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotComprehensiveValue
> ### Title: Plot comprehensive values of altarnatives
> ### Aliases: plotComprehensiveValue
> 
> ### ** Examples
> 
> perf <- matrix(c(5, 2, 1, 7, 0.5, 0.9, 0.4, 0.4), ncol = 2)
> problem <- buildProblem(perf, 3, FALSE, c('c', 'g'), c(3, 3))
> problem <- addAssignmentsLB(problem, c(1, 2), c(2, 3))
> 
> representativeFunction <- findRepresentativeFunction(problem, 0)
> plotComprehensiveValue(representativeFunction)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rosetta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fanova
> ### Title: Flexible anova
> ### Aliases: fanova
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> 
> ### Oneway anova with a plot
> fanova(dat=mtcars, y='mpg', between='cyl', plot=TRUE);
Flexible Analysis of Variance was called with:

  Dependent variable: mpg
  Factors: cyl

Between-subjects factor 'cyl' does not have class 'factor' in dataframe 'mtcars'. Converting it now.

Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rotations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nickel
> ### Title: Nickel electron backscatter diffraction data set
> ### Aliases: nickel
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(nickel) #Load the dataset
> Rep1 <- subset(nickel, rep == 1) #Subset the data to include only the first scan
> 
> #Get a rough idea of how the grain map looks by plotting the first 
> #element of the rotation matrix at each location
> qplot(xpos, ypos, data = Rep1, colour = V1, size = I(2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rotations-intro.Rnw’ using knitr
Quitting from lines 294-297 (rotations-intro.Rnw) 
Error: processing vignette 'rotations-intro.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rotations-intro.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnalysisResults_plot
> ### Title: Analysis Results Plotting - Conditional Power Plot
> ### Aliases: AnalysisResults_plot plot.AnalysisResults
> 
> ### ** Examples
> 
> 
> design <- getDesignGroupSequential(kMax = 2)
> 
> dataExample <- getDataset(
+     n = c(20, 30),
+ 	   means = c(50, 51),
+ 	   stDevs = c(130, 140)
+ )
> 
> result <- getAnalysisResults(design = design, 
+ 	   dataInput = dataExample, thetaH0 = 20, 
+ 	   nPlanned = c(30), thetaH1 = 1.5, stage = 1) 
[PROGRESS] Stage results calculated [0.0385 secs] 
[PROGRESS] Conditional power calculated [0.0035 secs] 
[PROGRESS] Conditional rejection probabilities (CRP) calculated [0.0014 secs] 
[PROGRESS] Repeated confidence interval of stage 1 calculated [1.1674 secs] 
[PROGRESS] Repeated confidence interval calculated [1.1689 secs] 
[PROGRESS] Overall repeated p-values of stage 1 calculated [0.4724 secs] 
[PROGRESS] Repeated p-values calculated [0.4738 secs] 
[PROGRESS] Final p-value calculated [0.0087 secs] 
[PROGRESS] Final confidence interval calculated [0.0313 secs] 
> 
> if (require(ggplot2)) plot(result, thetaRange = c(0, 100))
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rpdo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
> 
> data(pdo)
> ggplot(data = subset(pdo, pdo$Month == 1), aes(x = Year, y = PDO)) +
+  geom_line() + ylab("January PDO Index")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RpeakChrom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vanDeemter
> ### Title: Characterization of chromatographic columns using vanDeemter
> ###   equations.
> ### Aliases: vanDeemter
> 
> ### ** Examples
> 
> ggmetoxi <- vanDeemter(col = parameters_col_metoxi, ext = parameters_ext,
+               dead = parameters_dead, length = 150, A = 6, B = 200, C = 0.04,
+               GG = TRUE, Foley = FALSE, do.plot = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: vanDeemter ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘customitem.Rmd’ using knitr
Loading required package: parallel
--- finished re-building ‘customitem.Rmd’

--- re-building ‘diagnostics.Rmd’ using knitr
Quitting from lines 49-78 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘flexmirt-plots.Rmd’ using knitr
Quitting from lines 37-64 (flexmirt-plots.Rmd) 
Error: processing vignette 'flexmirt-plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘flexmirt-plots.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics.Rmd’ ‘flexmirt-plots.Rmd’

Error: Vignette re-building 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-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Quitting from lines 29-33 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘visualization.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostics.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 58-59 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘user_guide.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 44-51 (user_guide.Rmd) 
Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics.Rmd’ ‘user_guide.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WOE_custom
> ### Title: Custom Binning Numeric Variables
> ### Aliases: WOE_custom
> 
> ### ** Examples
> 
> mydata <- ISLR::Default
> mydata$default <- ifelse(mydata$default=="Yes", 1, 0) ## target coded with 1, 0
> WC_1 <- WOE_custom(dataset=mydata, var="balance", target = "default",
+            breaks=seq(0,3000,1000))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: WOE_custom ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rpsftm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rpsftm
> ### Title: Plot Method
> ### Aliases: plot.rpsftm
> 
> ### ** Examples
> 
> fit <- rpsftm(Surv(progyrs, prog)~rand(imm,1-xoyrs/progyrs),immdef, censyrs)
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpsftm_vignette.Rmd’ using rmarkdown
Quitting from lines 141-143 (rpsftm_vignette.Rmd) 
Error: processing vignette 'rpsftm_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rpsftm_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CoupledHarmonics.Rmd’ using rmarkdown
Quitting from lines 40-42 (CoupledHarmonics.Rmd) 
Error: processing vignette 'CoupledHarmonics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CoupledHarmonics.Rmd’

--- re-building ‘CoupledHarmonics2.Rmd’ using rmarkdown
Quitting from lines 40-42 (CoupledHarmonics2.Rmd) 
Error: processing vignette 'CoupledHarmonics2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CoupledHarmonics2.Rmd’

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

SUMMARY: processing the following files failed:
  ‘CoupledHarmonics.Rmd’ ‘CoupledHarmonics2.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataChart
> ### Title: Visualization of data characteristics.
> ### Aliases: dataChart
> 
> ### ** Examples
> 
> data(mlLatest100k)
> 
> a <- defineData(mlLatest100k)
There are values smaller that the defined threshold. If you want to keep using them please redefine the "minimum" argument.
> 
> dataChart(a, x = "items", y = "num_of_ratings")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: regbar
> ### Title: Barplot with explicit data comparison
> ### Aliases: regbar
> 
> ### ** Examples
> 
> # basic usage
> library("rreg")
> regbar(data = hfdata, x = inst, y = case2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pairwise_plot
> ### Title: Pairwise Plots
> ### Aliases: pairwise_plot
> 
> ### ** Examples
> 
> data(pendigits)
> digits_features <- pendigits[,1:34]
> digits_class <- pendigits[,35]
> pairwise_plot(digits_features, digits_class, type = "pca", pair_x = 1, pair_y = 3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pairwise_plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrr.Rmd’ using rmarkdown
Quitting from lines 89-90 (rrr.Rmd) 
Error: processing vignette 'rrr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rrr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rescaling_data.Rmd’ using rmarkdown
Quitting from lines 36-42 (rescaling_data.Rmd) 
Error: processing vignette 'rescaling_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rescaling_data.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_2ggplots
> ### Title: Add two ggplots into a document object
> ### Aliases: add_2ggplots
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> require(magrittr)
Loading required package: magrittr
> require(officer)
Loading required package: officer
> require(rvg)
Loading required package: rvg
> plot1 <- "ggplot(data = iris, aes(Sepal.Length, Petal.Length)) + geom_point()"
> plot2 <- "ggplot(data = iris, aes(Sepal.Length, Petal.Length, color = Species)) + geom_point()"
> read_pptx() %>% add_text(title="Two ggplots") %>% add_2ggplots(plot1=plot1,plot2=plot2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: %>% ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrtable.Rmd’ using rmarkdown
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 98-99 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rrtable.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.rsplit
> ### Title: Tidy Resampling Object
> ### Aliases: tidy.rsplit tidy.rset tidy.vfold_cv tidy.nested_cv
> 
> ### ** Examples
> 
> library(ggplot2)
> theme_set(theme_bw())
> 
> set.seed(4121)
> cv <- tidy(vfold_cv(mtcars, v = 5))
> ggplot(cv, aes(x = Fold, y = Row, fill = Data)) + 
+   geom_tile() + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basics.Rmd’ using rmarkdown
Loading required package: tidyr
--- finished re-building ‘Basics.Rmd’

--- re-building ‘Working_with_rsets.Rmd’ using rmarkdown
Loading required package: tidyr
Quitting from lines 131-134 (Working_with_rsets.Rmd) 
Error: processing vignette 'Working_with_rsets.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Working_with_rsets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.multisimsum
> ### Title: autoplot method for multisimsum objects
> ### Aliases: autoplot.multisimsum
> 
> ### ** Examples
> 
> data("frailty", package = "rsimsum")
> ms <- multisimsum(
+   data = frailty,
+   par = "par", true = c(trt = -0.50, fv = 0.75),
+   estvarname = "b", se = "se", methodvar = "model",
+   by = "fv_dist", x = TRUE
+ )
'ref' method was not specified, Cox, Gamma set as the reference
> 
> library(ggplot2)
> autoplot(ms, par = "trt")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 216-223 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘plotting.Rmd’ using rmarkdown
Quitting from lines 75-76 (plotting.Rmd) 
Error: processing vignette 'plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotting.Rmd’

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

--- re-building ‘rsimsumtidyverse.Rmd’ using rmarkdown
Quitting from lines 43-53 (rsimsumtidyverse.Rmd) 
Error: processing vignette 'rsimsumtidyverse.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rsimsumtidyverse.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘resource_suitability.Rmd’ using rmarkdown
Loading required package: rsMove
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Loading required package: ggplot2
Loading required package: knitr
Loading required package: kableExtra
Loading required package: caret
Loading required package: lattice
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: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    margin

Loading required package: e1071

Attaching package: 'e1071'

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

    interpolate

Quitting from lines 181-183 (resource_suitability.Rmd) 
Error: processing vignette 'resource_suitability.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘resource_suitability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
Quitting from lines 176-185 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘benchmark.Rmd’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CrossValidationSSL
> ### Title: Cross-validation in semi-supervised setting
> ### Aliases: CrossValidationSSL CrossValidationSSL.list
> ###   CrossValidationSSL.matrix
> 
> ### ** Examples
> 
> X <- model.matrix(Species~.-1,data=iris)
> y <- iris$Species
> 
> classifiers <- list("LS"=function(X,y,X_u,y_u) {
+   LeastSquaresClassifier(X,y,lambda=0)}, 
+   "EM"=function(X,y,X_u,y_u) {
+     SelfLearning(X,y,X_u,
+                  method=LeastSquaresClassifier)}
+ )
> 
> measures <- list("Accuracy" =  measure_accuracy,
+                  "Loss" = measure_losstest,
+                  "Loss labeled" = measure_losslab,
+                  "Loss Lab+Unlab" = measure_losstrain
+ )
> 
> # Cross-validation making sure test folds are non-overlapping
> cvresults1 <- CrossValidationSSL(X,y, 
+                                  classifiers=classifiers, 
+                                  measures=measures,
+                                  leaveout="test", k=10,
+                                  repeats = 2,n_labeled = 10)
> print(cvresults1)
CrossValidation object

Classifiers:
 	 LS
	 EM 
Measures:
 	 Accuracy
	 Loss
	 Loss labeled
	 Loss Lab+Unlab
	 Time 
10  folds
2  repeats
0  missing
> plot(cvresults1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘aov.Rmd’ using rmarkdown
--- finished re-building ‘aov.Rmd’

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

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

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

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

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

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

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

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

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

--- re-building ‘priors.Rmd’ using rmarkdown
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().
Quitting from lines 227-236 (priors.Rmd) 
Error: processing vignette 'priors.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘priors.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘external.Rmd’ using rmarkdown
--- finished re-building ‘external.Rmd’

--- re-building ‘rstan.Rmd’ using rmarkdown
Quitting from lines 364-365 (rstan.Rmd) 
Error: processing vignette 'rstan.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rstan.Rmd’

--- re-building ‘stanfit-objects.Rmd’ using rmarkdown
--- finished re-building ‘stanfit-objects.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coregisterImages
> ### Title: Image to Image Co-Registration based on Mutual Information
> ### Aliases: coregisterImages
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
> library(ggplot2)
> library(reshape2)
> data(rlogo)
> reference <- rlogo
> ## Shift reference 2 pixels to the right and 3 up
> missreg <- shift(reference, x = 2, y = 3)
> 
> ## Compare shift
> p <- ggR(reference, sat = 1, alpha = .5) 
> p + ggR(missreg, sat = 1, hue = .5, alpha = 0.5, ggLayer=TRUE) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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-patched-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Running examples in ‘rsvd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_pdf rsvg_png rsvg_ps rsvg_raw rsvg_svg rsvg_webp
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RSwissMaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: can.plot
> ### Title: Plotting canton-level maps of Switzerland
> ### Aliases: can.plot
> 
> ### ** Examples
> 
>  # Generating sample data:
>  dt <- can.template(2016)
>  for(i in 1:nrow(dt)){dt$values[i] <- sample(c(300:700), 1)/1000}
> 
>  # Plotting sample data:
>  can.plot(dt$bfs_nr, dt$values, 2016)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 33-35 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building 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-patched-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rtf.Rnw’ using Sweave

Error: processing vignette 'rtf.Rnw' failed with diagnostics:
 chunk 29 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘rtf.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_output
> ### Title: Uses output file from MicroPEM to create a 'micropem' object.
> ### Aliases: convert_output
> 
> ### ** Examples
> 
> micropem_example <- convert_output(system.file('extdata', 'CHAI.csv', package = 'rtimicropem'))
> micropem_example$plot()
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chai_data_cleaning.Rmd’ using rmarkdown
--- finished re-building ‘chai_data_cleaning.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 86-88 (vignette_ammon.Rmd) 
Error: processing vignette 'vignette_ammon.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_ammon.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘transfer-entropy.Rmd’ using rmarkdown
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
Quitting from lines 240-241 (transfer-entropy.Rmd) 
Error: processing vignette 'transfer-entropy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘transfer-entropy.Rmd’

SUMMARY: processing the following file failed:
  ‘transfer-entropy.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rubias-overview.Rmd’ using rmarkdown
Quitting from lines 275-292 (rubias-overview.Rmd) 
Error: processing vignette 'rubias-overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rubias-overview.Rmd’

--- re-building ‘rubias-underlying-data-structures.Rmd’ using rmarkdown
--- finished re-building ‘rubias-underlying-data-structures.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_path
> ### Title: Plot a path of the simulated ruin process
> ### Aliases: plot_path
> 
> ### ** Examples
> 
> model <- CramerLundberg(initial_capital = 10,
+                         premium_rate = 1,
+                         claim_poisson_arrival_rate = 1,
+                         claim_size_generator = rexp,
+                         claim_size_parameters = list(rate = 1))
> 
> path <- simulate_path(model = model, max_time_horizon = 10)
> 
> plot_path(path)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ruin-intro.Rmd’ using rmarkdown
Set default RNG to L'Ecuyer-CMRG for a safe parallel simulation.
Quitting from lines 77-78 (ruin-intro.Rmd) 
Error: processing vignette 'ruin-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ruin-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-runstats.Rmd’ using rmarkdown
Quitting from lines 176-192 (using-runstats.Rmd) 
Error: processing vignette 'using-runstats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-runstats.Rmd’

SUMMARY: processing the following file failed:
  ‘using-runstats.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw
> ### Title: Beautiful graphical representation of multiplication tables
> ### Aliases: draw
> 
> ### ** Examples
> 
> draw(table=2,modulo = 10, label=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.vinecop_dist
> ### Title: Plotting 'vinecop_dist' and 'vinecop' objects.
> ### Aliases: plot.vinecop_dist contour.vinecop_dist plot.vinecop
> ###   contour.vinecop plot.vinecop contour.vinecop_dist contour.vinecop
> ### Keywords: plot
> 
> ### ** Examples
> 
> # set up vine copula model
> d <- 20
> n <- 2e2
> u <- matrix(runif(n*d), n, d)
> vc <- vinecop(u, "indep")
> 
> # plot
> plot(vc, tree = c(1,2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  ── 1. Error: plot functions work (@test_vinecop_dist.R#78)  ────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(p <- plot(vc, edge_labels = "family", var_names = "legend")) at testthat/test_vinecop_dist.R:78
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plot(vc, edge_labels = "family", var_names = "legend")
  10: plot.vinecop_dist(vc, edge_labels = "family", var_names = "legend")
  ...
  18: preDraw(x)
  19: preDraw.gTree(x)
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.viewport(X[[i]], ...)
  27: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 227 SKIPPED: 0 FAILED: 1
  1. Error: plot functions work (@test_vinecop_dist.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Running examples in ‘RWeka-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Weka_classifier_trees
> ### Title: R/Weka Classifier Trees
> ### Aliases: Weka_classifier_trees J48 LMT M5P DecisionStump plot.Weka_tree
> ###   parse_Weka_digraph
> ### Keywords: models regression classif tree
> 
> ### ** Examples
> 
> m1 <- J48(Species ~ ., data = iris)
> 
> ## print and summary
> m1
J48 pruned tree
------------------

Petal.Width <= 0.6: setosa (50.0)
Petal.Width > 0.6
|   Petal.Width <= 1.7
|   |   Petal.Length <= 4.9: versicolor (48.0/1.0)
|   |   Petal.Length > 4.9
|   |   |   Petal.Width <= 1.5: virginica (3.0)
|   |   |   Petal.Width > 1.5: versicolor (3.0/1.0)
|   Petal.Width > 1.7: virginica (46.0/1.0)

Number of Leaves  : 	5

Size of the tree : 	9

> summary(m1) # calls evaluate_Weka_classifier()

=== Summary ===

Correctly Classified Instances         147               98      %
Incorrectly Classified Instances         3                2      %
Kappa statistic                          0.97  
Mean absolute error                      0.0233
Root mean squared error                  0.108 
Relative absolute error                  5.2482 %
Root relative squared error             22.9089 %
Total Number of Instances              150     

=== Confusion Matrix ===

  a  b  c   <-- classified as
 50  0  0 |  a = setosa
  0 49  1 |  b = versicolor
  0  2 48 |  c = virginica
> table(iris$Species, predict(m1)) # by hand
            
             setosa versicolor virginica
  setosa         50          0         0
  versicolor      0         49         1
  virginica       0          2        48
> 
> ## visualization
> ## use partykit package
> if(require("partykit", quietly = TRUE)) plot(m1)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RxODE-covariates.Rmd’ using rmarkdown
Quitting from lines 73-75 (RxODE-covariates.Rmd) 
Error: processing vignette 'RxODE-covariates.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-covariates.Rmd’

--- re-building ‘RxODE-data-frame.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-data-frame.Rmd’

--- re-building ‘RxODE-events.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-events.Rmd’

--- re-building ‘RxODE-intro.Rmd’ using rmarkdown
Quitting from lines 134-137 (RxODE-intro.Rmd) 
Error: processing vignette 'RxODE-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-intro.Rmd’

--- re-building ‘RxODE-mix-lin-ode.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-mix-lin-ode.Rmd’

--- re-building ‘RxODE-shiny.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-shiny.Rmd’

--- re-building ‘RxODE-sim-var.Rmd’ using rmarkdown
Quitting from lines 50-63 (RxODE-sim-var.Rmd) 
Error: processing vignette 'RxODE-sim-var.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-sim-var.Rmd’

--- re-building ‘RxODE-stiff.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-stiff.Rmd’

--- re-building ‘RxODE-syntax.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-syntax.Rmd’

--- re-building ‘RxODE-transit-compartments.Rmd’ using rmarkdown
Quitting from lines 26-51 (RxODE-transit-compartments.Rmd) 
Error: processing vignette 'RxODE-transit-compartments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-transit-compartments.Rmd’

SUMMARY: processing the following files failed:
  ‘RxODE-covariates.Rmd’ ‘RxODE-intro.Rmd’ ‘RxODE-sim-var.Rmd’
  ‘RxODE-transit-compartments.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qqnorm_spss
> ### Title: SPSS like QQ-plot
> ### Aliases: qqnorm_spss
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> 
> set.seed(0)
> x <- sample(0:9, 100, rep=TRUE)
> 
> ### SPSS like
> 
> # Standard QQ-plot
> qq <- qqnorm_spss(x, 1)
> plot(qq)  
> ggplot(qq)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 90-104 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sentiment.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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-patched-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sadists.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: grid
Loading required package: polynom
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette 'sadists.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sadists.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rfh
> ### Title: Plots
> ### Aliases: plot.rfh plot.prediction.fitrfh plot.mse.fitrfh qqPlot
> ###   blandAltmanPlot
> 
> ### ** Examples
> 
> qqPlot(rnorm(10))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘glue.Rnw’ using Sweave
--- finished re-building ‘glue.Rnw’

--- re-building ‘sc-intro.Rnw’ using Sweave
Simulation started at 2019-03-29 19:23:31.
N2,rho=0.7 Adaptive Metropolis: 557 (156,Inf) evals tuning=0.1; act.y=92.7
Gamma2 Adaptive Metropolis: 649 (155,Inf) evals tuning=0.1; act.y=9.88
N2,rho=0.7 ARMS: 676 (294,9.87e+03) evals tuning=0.1; act.y=5.93
Gamma2 ARMS: 17.8 (11.1,32.3) evals tuning=0.1; act.y=2.01
N2,rho=0.7 Adaptive Metropolis: 13.3 (8.53,21.8) evals tuning=1; act.y=6.6
Gamma2 Adaptive Metropolis: 65.8 (25.6,Inf) evals tuning=1; act.y=9.42
Gamma2 ARMS: 7.01 (5.17,9.83) evals tuning=1; act.y=1.29
N2,rho=0.7 ARMS: 656 (288,4.41e+04) evals tuning=1; act.y=9.88
N2,rho=0.7 Adaptive Metropolis: 250 (69.6,Inf) evals tuning=10; act.y=44.8
N2,rho=0.7 ARMS: 2.73e+03 (893,Inf) evals tuning=10; act.y=28.4
Gamma2 Adaptive Metropolis: 76.2 (35.8,Inf) evals tuning=10; act.y=3.16
Gamma2 ARMS: 12.7 (9.13,16.9) evals tuning=10; act.y=0.999
N2,rho=0.7 Adaptive Metropolis: NA (NA,NA) evals tuning=100; act.y=NA
Gamma2 Adaptive Metropolis: 644 (154,Inf) evals tuning=100; act.y=96.5
Gamma2 ARMS: 12.2 (9.13,16.3) evals tuning=100; act.y=0.94
N2,rho=0.7 ARMS: 1.34e+03 (530,Inf) evals tuning=100; act.y=15
Simulation finished at 2019-03-29 19:23:35.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.

Error: processing vignette 'sc-intro.Rnw' failed with diagnostics:
 chunk 1 
Error in Summary.unit(structure(c(3.2, 3.2), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘sc-intro.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_eigen_DFoverlay_list
> ### Title: Plot for each eigenSpline the automatically fitted spline,
> ###   splines for all df and a spline at a chosen df
> ### Aliases: get_eigen_DFoverlay_list
> 
> ### ** Examples
> 
> ## 8 subjects, 4 time-points, 3 variables
> inputData  <- acuteInflammation$data[0:32,1:3]
> ind        <- acuteInflammation$meta$ind[0:32]
> time       <- acuteInflammation$meta$time[0:32]
> eigen      <- get_eigen_spline(inputData, ind, time, nPC=NA, scaling="scaling_UV",
+                                method="nipals", verbose=TRUE, centering=TRUE, ncores=0)
nipals calculated PCA
Importance of component(s):
                 PC1     PC2      PC3
R2            0.9272 0.06606 0.006756
Cumulative R2 0.9272 0.99324 1.000000
total time: 0.07 secs
> paramSpace <- get_param_evolution(eigen, step=1)
> plotList   <- get_eigen_DFoverlay_list(eigen,manualDf=3,step=0.5,showPt=TRUE,autofit=TRUE)
> plotList[1]
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-command-line-functions.Rmd’ using rmarkdown
Quitting from lines 122-132 (advanced-command-line-functions.Rmd) 
Error: processing vignette 'advanced-command-line-functions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘advanced-command-line-functions.Rmd’

--- re-building ‘automated-command-line.Rmd’ using rmarkdown
--- finished re-building ‘automated-command-line.Rmd’

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

--- re-building ‘plotting-options.Rmd’ using rmarkdown
Quitting from lines 38-46 (plotting-options.Rmd) 
Error: processing vignette 'plotting-options.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotting-options.Rmd’

--- re-building ‘prepare-input-data.Rmd’ using rmarkdown
--- finished re-building ‘prepare-input-data.Rmd’

--- re-building ‘selecting-optimal-df.Rmd’ using rmarkdown
Quitting from lines 124-181 (selecting-optimal-df.Rmd) 
Error: processing vignette 'selecting-optimal-df.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘selecting-optimal-df.Rmd’

--- re-building ‘theoretical-background.Rmd’ using rmarkdown
Quitting from lines 82-133 (theoretical-background.Rmd) 
Error: processing vignette 'theoretical-background.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘theoretical-background.Rmd’

--- re-building ‘santaR-GUI.pdf.asis’ using asis
--- finished re-building ‘santaR-GUI.pdf.asis’

SUMMARY: processing the following files failed:
  ‘advanced-command-line-functions.Rmd’ ‘plotting-options.Rmd’
  ‘selecting-optimal-df.Rmd’ ‘theoretical-background.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: histogramplot
> ### Title: Plot a generic histogram
> ### Aliases: histogramplot
> 
> ### ** Examples
> 
> a <- as.data.frame(rnorm(100))
> histogramplot(dfCol=a)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 90-105 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scat
> ### Title: Scatterplot
> ### Aliases: scat
> 
> ### ** Examples
> 
> set.seed(1337)
> 
> X <- rnorm(100)
> Y <- 0.5*X + rnorm(100)
> dat <- data.frame(X = X, Y = Y)
> 
> scat(dat, x = 'X', y = 'Y', line = 'linear', se = TRUE, marg = 'dens')
Loading required namespace: jmvcore
Loading required namespace: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘scatterpie-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_scatterpie
> ### Title: geom_scatterpie
> ### Aliases: geom_scatterpie
> 
> ### ** Examples
> 
> library(ggplot2)
> d <- data.frame(x=rnorm(5), y=rnorm(5))
> d$A <- abs(rnorm(5, sd=1))
> d$B <- abs(rnorm(5, sd=2))
> d$C <- abs(rnorm(5, sd=3))
> ggplot() + geom_scatterpie(aes(x=x, y=y), data=d, cols=c("A", "B", "C")) + coord_fixed()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘scatterpie.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 49-51 (scatterpie.Rmd) 
Error: processing vignette 'scatterpie.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘scatterpie.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Estimating-effect-sizes.Rmd’ using rmarkdown
Loading required package: nlme
Quitting from lines 147-161 (Estimating-effect-sizes.Rmd) 
Error: processing vignette 'Estimating-effect-sizes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Estimating-effect-sizes.Rmd’

SUMMARY: processing the following file failed:
  ‘Estimating-effect-sizes.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘scholar.Rmd’ using rmarkdown
Quitting from lines 70-76 (scholar.Rmd) 
Error: processing vignette 'scholar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘scholar.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2-scales
> ### Title: Scales to use for ggplot2
> ### Aliases: ggplot2-scales scale_colour_scico scale_color_scico
> ###   scale_fill_scico scale_colour_scico_d scale_color_scico_d
> ###   scale_fill_scico_d
> 
> ### ** Examples
> 
> 
> if (require('ggplot2')) {
+   volcano <- data.frame(
+     x = rep(seq_len(ncol(volcano)), each = nrow(volcano)),
+     y = rep(seq_len(nrow(volcano)), ncol(volcano)),
+     height = as.vector(volcano)
+   )
+   
+   ggplot(volcano, aes(x = x, y = y, fill = height)) + 
+     geom_raster() + 
+     scale_fill_scico(palette = 'tokyo') 
+     
+   ggplot(iris, aes(x=Petal.Width, y=Petal.Length)) +
+     geom_point(aes(color=Species), size=10) + 
+     scale_colour_scico_d() 
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
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-patched-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Running examples in ‘scmamp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensities
> ### Title: Kernel based density estimation of the samples
> ### Aliases: plotDensities
> 
> ### ** Examples
> 
> data(data_gh_2010)
> plotDensities(data.gh.2010)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_loading_and_manipulation.Rmd’ using rmarkdown
--- finished re-building ‘Data_loading_and_manipulation.Rmd’

--- re-building ‘Statistical_assessment_of_the_differences.Rmd’ using rmarkdown
Quitting from lines 47-48 (Statistical_assessment_of_the_differences.Rmd) 
Error: processing vignette 'Statistical_assessment_of_the_differences.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Statistical_assessment_of_the_differences.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyzeClones
> ### Title: Clonal assignment analysis
> ### Aliases: analyzeClones
> 
> ### ** Examples
> 
> # Clonal assignment analysis
> results <- analyzeClones(ClonedExampleDb, junction = "JUNCTION", v_call = "V_CALL",
+                           j_call = "J_CALL", clone = "CLONE", first = TRUE)
> # print threshold (a numeric)
> results@threshold
[1] 0.23
> 
> # get inter and intra conal distances (a data.frame)
> df <- results@inter_intra[[1]]
> 
> # density plot of inter versus intra clonal distances  (a ggplot).
> results@plot_inter_intra
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Scoper-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 162-175 (Scoper-Vignette.Rmd) 
Error: processing vignette 'Scoper-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Scoper-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Scoper-Vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: woebin_plot
> ### Title: WOE Binning Visualization
> ### Aliases: woebin_plot
> 
> ### ** Examples
> 
> # Load German credit data
> data(germancredit)
> 
> # Example I
> bins1 = woebin(germancredit, y="creditability", x="credit.amount")
[INFO] creating woe binning ... 
> 
> p1 = woebin_plot(bins1)
> print(p1)
$credit.amount
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SCORPIUS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_trajectory_plot
> ### Title: Visualise SCORPIUS
> ### Aliases: draw_trajectory_plot
> 
> ### ** Examples
> 
> ## Generate a synthetic dataset
> dataset <- generate_dataset(type="p", num_genes=500, num_samples=300, num_groups=4)
> space <- reduce_dimensionality(dataset$expression, correlation_distance, ndim=2)
> groups <- dataset$sample_info$group_name
> 
> ## Simply plot the samples
> draw_trajectory_plot(space)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ginhoux.Rmd’ using rmarkdown
Quitting from lines 66-67 (ginhoux.Rmd) 
Error: processing vignette 'ginhoux.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ginhoux.Rmd’

--- re-building ‘simulated-data.Rmd’ using rmarkdown
Quitting from lines 68-69 (simulated-data.Rmd) 
Error: processing vignette 'simulated-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulated-data.Rmd’

SUMMARY: processing the following files failed:
  ‘ginhoux.Rmd’ ‘simulated-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Details.Rmd’ using knitr
--- finished re-building ‘Details.Rmd’

--- re-building ‘Tutorial.Rmd’ using knitr
Loading required package: Rcpp
Loading required package: RcppProgress
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 129-134 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 43-47 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scRNAtools-package
> ### Title: Single Cell RNA Sequencing Data Analysis Tools
> ### Aliases: scRNAtools-package
> 
> ### ** Examples
> 
> ####Here list three main function, cluster, PCA and t-SNE####
> ####cluster####
> data(example1);##Example data in this package.
> k<-6;##set K based on your own requirement.
> scRNAtools_cluster(example1,k)
end fraction
clustered
clustered
clustered
clustered
clustered
> ####PCA####
> data(example1)
> data(types)
> pdf(file=file.path(tempdir(), "PCA_result-R.pdf"))##Save the figures of PCA results.
> scRNAtools_pca(example1,types)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SDaA_using_survey.Rnw’ using Sweave
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart


Attaching package: ‘ggplot2’

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

    seals


Error: processing vignette 'SDaA_using_survey.Rnw' failed with diagnostics:
 chunk 24 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘SDaA_using_survey.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: localSuppression
> ### Title: Local Suppression to obtain k-anonymity
> ### Aliases: localSuppression kAnon
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(francdat)
> ## Local Suppression
> localS <- localSuppression(francdat, keyVar=c(4,5,6))
> localS

-----------------------
Total number of suppressions in the key variables: 4 (new: 4)

Number of suppressions by key variables:
(in parenthesis, the total number suppressions is shown)

   Key2  Key3  Key4
1 1 (1) 0 (0) 3 (3)

2-anonymity == TRUE
-----------------------
> plot(localS)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sdmpredictors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
> print(p)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif’
Content type 'image/tiff' length 2518560 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_salinity_lonlat.tif’
Content type 'image/tiff' length 5841760 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_ph.tif’
Content type 'image/tiff' length 3201193 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

Quitting from lines 136-163 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio1.bil" 
[2] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio11.bil"
[3] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio12.bil"
[4] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio14.bil"
[5] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio16.bil"
[6] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio5.bil" 
[7] "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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-patched-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-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Running examples in ‘season-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: third
> ### Title: Third-order Moment
> ### Aliases: third
> 
> ### ** Examples
> 
> data(CVD)
> third(CVD$cvd, n.lag=12)
Maximum at (including symmetries)
0 0 
Minimum at (including symmetries)
-8 8 0 -8 0 8 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: third ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘season-vignette.Rmd’ using rmarkdown
Quitting from lines 32-38 (season-vignette.Rmd) 
Error: processing vignette 'season-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘season-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘segclust2d-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: segclust
> ### Title: Segmentation/Clustering of movement data - Generic function
> ### Aliases: segclust segclust.data.frame segclust.Move segclust.ltraj
> 
> ### ** Examples
> 
> #' @examples
> df <-  test_data()$data
> #' # data is a data.frame with column 'x' and 'y'
> # Simple segmentation with automatic subsampling if data has more than 1000 rows:
> res <- segclust(df, Kmax = 15, lmin = 10, ncluster = 2:4, seg.var = c("x","y"))
Rescaling variables - you can disable this with scale.variable = FALSE
Segmenting - 2 class
Smoothing  - 2 class
Segmenting - 3 class
Smoothing  - 3 class
Segmenting - 4 class
Smoothing  - 4 class
>  # Plot results
>  plot(res)
BIC-selected number of class : 3 class.
BIC-selected number of segment : 6
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘selfea-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_statistics_from_dataFrame
> ### Title: get_statistics_from_dataFrame
> ### Aliases: get_statistics_from_dataFrame
> 
> ### ** Examples
> 
> library(selfea)
> 
> ## Test selfea for single protein expression
> values <- c(6,8,10,29,26,22)
> groups <- c("U200","U200","U200","U600","U600","U600")
> experiments <- c("exp1","exp2","exp3","exp4","exp5","exp6")
> 
> df_expr <- data.frame(ID="Protein_1",exp1=6,exp2=8,exp3=10,exp4=29,exp5=26,exp6=22)
> df_group <- data.frame(Col_Name=experiments,Group=groups)
> list_result <- get_statistics_from_dataFrame(df_expr,df_group)
Expression data dimension:	1 IDs x 6 Columns
You chose "fdr" for p-value adjustment.

Group dimension:
				Group U200 has 3 replicates
				Group U600 has 3 replicates
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
> top_table(list_result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: top_table ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sensitivityCalibration-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calibrate_one
> ### Title: Make the calibration plot.
> ### Aliases: calibrate_one
> 
> ### ** Examples
> 
> data(NHANES_blood_lead_small_matched)
> attach(NHANES_blood_lead_small_matched)
> 
> # Prepare the lambda_vec and delta_vec
> lambda_vec = c(seq(0.1,1.9,0.1), 2.2, 2.5, 3, 3.5, 4)
> delta_vec = c(7.31, 5.34, 4.38, 3.76, 3.18, 2.87, 2.55, 2.36, 2.16, 1.99, 1.86,
+ 1.74, 1.63, 1.54, 1.44, 1.40, 1.31, 1.28, 1.22, 1.08, 0.964, 0.877, 0.815, 0.750)
> 
> calibrate_one(lambda_vec, delta_vec, 9, c(1,0), c(0.5,0.5), 1, 0.492,
+ colnames(NHANES_blood_lead_small_matched)[1:8], NHANES_blood_lead_small_matched)
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sensitivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: support
> ### Title: Support index functions: Measuring the effect of input variables
> ###   over their support
> ### Aliases: support
> 
> ### ** Examples
> 
> 
> # -----------------
> # ishigami function
> # -----------------
> n <- 5000
> n.points <- 1000
> d <- 3
> 
> set.seed(0)
> X <- matrix(runif(d*n, min = -pi, max = pi), n, d)
> Xnew <- matrix(seq(from = -pi, to = pi, length=n.points), n.points, d)
> 
> b <- support(model = ishigami.fun, X, Xnew)
> 
> # plot method (x-axis in probability scale), of the normalized support index functions
> plot(b, col = c("lightskyblue4", "lightskyblue1", "black"), 
+      xprob = TRUE, p = 'punif', p.arg = list(min = -pi, max = pi), ylim = c(0, 2))
> 
> # below : diagonal scatterplots of the gradient, 
> # on which are based the estimation by smoothing
> scatterplot(b, xprob = TRUE) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: scatterplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SensMixed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: function creates plots for the sensmixed object
> ### Aliases: plot.sensmixed
> 
> ### ** Examples
> 
> res <- sensmixed(c("Coloursaturation", "Colourbalance", "Noise"),
+                   prod_effects=c("TVset", "Picture"), 
+                   assessor="Assessor", data=TVbo, MAM=TRUE, 
+                   control=list(reduce.random=FALSE))

  |                                                                            
  |                                                                      |   0%fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |=======================                                               |  33%fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |===============================================                       |  67%Warning: 
 Random term (1 | TVset:Assessor) was eliminated because of standard deviation being equal to 0 

Warning: 
 Random term (1 | TVset:Picture:Assessor) was eliminated because of standard deviation being equal to 0 

fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |======================================================================| 100%
> plot(res, isRand = TRUE)
Using effs, effs_short, abbreffs as id variables
Using effs as id variables
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sensobol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_scatter
> ### Title: Scatterplots of the model output against the model inputs
> ### Aliases: plot_scatter
> 
> ### ** Examples
> 
> # Define settings:
> n <- 100; k <- 8; R <- 10
> # Design the sample matrix:
> A <- sobol_matrices(n = n, k = k, second = TRUE, third = TRUE)
> # Compute the model output:
> Y <- sobol_Fun(A)
> # Plot scatterplots:
> plot_scatter(x = A, Y = Y, n = n, params = colnames(data.frame(A)))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sensobol.Rmd’ using rmarkdown
Quitting from lines 53-57 (sensobol.Rmd) 
Error: processing vignette 'sensobol.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sensobol.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateDictionary
> ### Title: Generates dictionary of decisive terms
> ### Aliases: generateDictionary generateDictionary.Corpus
> ###   generateDictionary.character generateDictionary.data.frame
> ###   generateDictionary.TermDocumentMatrix
> ###   generateDictionary.DocumentTermMatrix
> ### Keywords: dictionary evaluation sentiment
> 
> ### ** Examples
> 
> # Create a vector of strings
> documents <- c("This is a good thing!",
+                "This is a very good thing!",
+                "This is okay.",
+                "This is a bad thing.",
+                "This is a very bad thing.")
> response <- c(1, 0.5, 0, -0.5, -1)
> 
> # Generate dictionary with LASSO regularization
> dictionary <- generateDictionary(documents, response)
> 
> # Show dictionary
> dictionary
Type: weighted (words with individual scores)
Intercept: 5.55333e-05
-0.51 bad
 0.51 good
> summary(dictionary)
Dictionary type:  weighted (words with individual scores)
Total entries:    2
Positive entries: 1 (50%)
Negative entries: 1 (50%)
Neutral entries:  0 (0%)

Details
Average score:      -5.251165e-05
Median:             -5.251165e-05
Min:                -0.5119851
Max:                0.5118801
Standard deviation: 0.7239821
Skewness:           0
> plot(dictionary)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SentimentAnalysis.Rmd’ using rmarkdown
Quitting from lines 67-91 (SentimentAnalysis.Rmd) 
Error: processing vignette 'SentimentAnalysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SentimentAnalysis.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sentomeasures
> ### Title: Plot sentiment measures
> ### Aliases: plot.sentomeasures
> 
> ### ** Examples
> 
> data("usnews", package = "sentometrics")
> data("list_lexicons", package = "sentometrics")
> data("list_valence_shifters", package = "sentometrics")
> 
> # construct a sentomeasures object to start with
> corpus <- sento_corpus(corpusdf = usnews)
> corpusSample <- quanteda::corpus_sample(corpus, size = 500)
> l <- sento_lexicons(list_lexicons[c("LM_en")], list_valence_shifters[["en"]])
> ctr <- ctr_agg(howTime = c("equal_weight", "linear"), by = "year", lag = 3)
> sentomeasures <- sento_measures(corpusSample, l, ctr)
> 
> # plot sentiment measures
> plot(sentomeasures, group = "features")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pimplot
> ### Title: Prime implicants, truth table rows, and necessity plots.
> ### Aliases: pimplot
> ### 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)
> 
> # Plot the prime implicants of the parsimonious solution:
> 
> pimplot(data = SCHF, results = sol_yp, outcome = "EXPORT")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pimplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Seurat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorTSNESplit
> ### Title: Color tSNE Plot Based on Split
> ### Aliases: ColorTSNESplit
> 
> ### ** Examples
> 
> pbmc_small
An object of class seurat in project SeuratProject 
 230 genes across 80 samples.
> PlotClusterTree(pbmc_small)
> ColorTSNESplit(pbmc_small, node = 6)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ColorTSNESplit ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Quitting from lines 172-175 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
--- finished re-building ‘sf6.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBoundary
> ### Title: A function to plot the boundary of the decision region
> ### Aliases: plotBoundary
> ### Keywords: design
> 
> ### ** Examples
> 
> plotBoundary(b1=2.8, b0=3.3, p=c(.5, .75))
Warning: Removed 2 rows containing missing values (geom_path).
Warning: Removed 4 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sgmodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_sgmod
> ### Title: plot_sgmod
> ### Aliases: plot_sgmod
> 
> ### ** Examples
> 
> model <- sgmodel( grid = 100, rho = 0.2, sigma = 0.02)
> plot_sgmod(model)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘sGMRFmix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_multivariate_data
> ### Title: Plot multivariate data
> ### Aliases: plot_multivariate_data
> 
> ### ** Examples
> 
> library(sGMRFmix)
> 
> test_data <- generate_test_data()
> test_label <- generate_test_labels()
> 
> plot_multivariate_data(test_data)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sGMRFmix.Rmd’ using rmarkdown
Quitting from lines 37-41 (sGMRFmix.Rmd) 
Error: processing vignette 'sGMRFmix.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sGMRFmix.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_shadowtext
> ### Title: geom_shadowtext
> ### Aliases: geom_shadowtext
> 
> ### ** Examples
> 
> library(ggplot2)
> d <- data.frame(x = rnorm(3), y=rnorm(3), label = c('hello', 'world', '!!!'))
> ggplot(d, aes(x,y)) + geom_shadowtext(aes(label=label, color=label), bg.colour='firebrick')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shadowtext.Rmd’ using rmarkdown
Quitting from lines 52-75 (shadowtext.Rmd) 
Error: processing vignette 'shadowtext.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘shadowtext.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distToNearest
> ### Title: Distance to nearest neighbor
> ### Aliases: distToNearest
> 
> ### ** Examples
> 
> # Subset example data to one sample as a demo
> data(ExampleDb, package="alakazam")
> db <- subset(ExampleDb, SAMPLE == "-1h")
> 
> # Use genotyped V assignments, Hamming distance, and normalize by junction length
> dist <- distToNearest(db, vCallColumn="V_CALL_GENOTYPED", model="ham", 
+                       first=FALSE, normalize="len")
>                            
> # Plot histogram of non-NA distances
> p1 <- ggplot(data=subset(dist, !is.na(DIST_NEAREST))) + 
+       theme_bw() + 
+       ggtitle("Distance to nearest: Hamming") + 
+       xlab("distance") +
+       geom_histogram(aes(x=DIST_NEAREST), binwidth=0.025, 
+                      fill="steelblue", color="white")
> plot(p1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown
Quitting from lines 69-72 (Dirichlet-elicitation.Rmd) 
Error: processing vignette 'Dirichlet-elicitation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Dirichlet-elicitation.Rmd’

--- re-building ‘Multivariate-normal-copula.Rmd’ using rmarkdown
Quitting from lines 50-53 (Multivariate-normal-copula.Rmd) 
Error: processing vignette 'Multivariate-normal-copula.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Multivariate-normal-copula.Rmd’

--- re-building ‘SHELF-overview.Rmd’ using rmarkdown
Quitting from lines 70-71 (SHELF-overview.Rmd) 
Error: processing vignette 'SHELF-overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SHELF-overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Dirichlet-elicitation.Rmd’ ‘Multivariate-normal-copula.Rmd’
  ‘SHELF-overview.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simulateEstimates
> ### Title: Simulates capture re-capture estimates
> ### Aliases: simulateEstimates
> 
> ### ** Examples
> 
> library(ggplot2)
> # Simulate estimates from the Mt model with no population heterogeneity
> ests <- simulateEstimates(15,500,c(.1,.1,.1))
> 
> # Simulate estimates from the Mth (Normal) model with no population heterogeneity.
> ests2 <- simulateEstimates(20,500,c(.1,.1,.1), htype="Normal")
> 
> df <- data.frame(est = ests[[1]],type="Mt")
> df <- rbind(df, data.frame(est = ests2[[1]],type="Mth (Normal)"))
> qplot(x=est, color=type, data=df, geom="density") +
+   geom_vline(xintercept=500,color="purple")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown
Quitting from lines 135-165 (Centroid-Vectors.Rmd) 
Error: processing vignette 'Centroid-Vectors.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Centroid-Vectors.Rmd’

--- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown
--- finished re-building ‘Customising-Plots-Manually.Rmd’

--- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown
--- finished re-building ‘Ellipse-Overlap.Rmd’

--- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown
--- finished re-building ‘Introduction-to-SIBER.Rmd’

--- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown
Quitting from lines 143-150 (Plot-posterior-ellipses.Rmd) 
Error: processing vignette 'Plot-posterior-ellipses.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Plot-posterior-ellipses.Rmd’

--- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown
--- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’

--- re-building ‘Test-convergence.Rmd’ using rmarkdown
--- finished re-building ‘Test-convergence.Rmd’

SUMMARY: processing the following files failed:
  ‘Centroid-Vectors.Rmd’ ‘Plot-posterior-ellipses.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 5 clusters
  ── 1. Failure: delay (@test-graph.R#50)  ───────────────────────────────────────
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigmoid.Rmd’ using rmarkdown
Quitting from lines 59-67 (sigmoid.Rmd) 
Error: processing vignette 'sigmoid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sigmoid.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_simpdf_theory
> ### Title: Plot Simulated Probability Density Function and Target PDF by
> ###   Distribution Name or Function for Continuous or Count Variables
> ### Aliases: plot_simpdf_theory
> ### Keywords: plot
> 
> ### ** Examples
> 
> # Using normal mixture variable from contmixvar1 example
> Nmix <- contmixvar1(n = 1000, "Polynomial", means = 0, vars = 1,
+   mix_pis = c(0.4, 0.6), mix_mus = c(-2, 2), mix_sigmas = c(1, 1),
+   mix_skews = c(0, 0), mix_skurts = c(0, 0), mix_fifths = c(0, 0),
+   mix_sixths = c(0, 0))
Total Simulation time: 0 minutes 
> plot_simpdf_theory(Nmix$Y_mix[, 1],
+   title = "Mixture of Normal Distributions",
+   fx = function(x) 0.4 * dnorm(x, -2, 1) + 0.6 * dnorm(x, 2, 1),
+   lower = -5, upper = 5)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cont_mixture.Rmd’ using rmarkdown
Quitting from lines 129-132 (cont_mixture.Rmd) 
Error: processing vignette 'cont_mixture.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cont_mixture.Rmd’

--- re-building ‘corr_mixture.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

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

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

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

--- re-building ‘workflow.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 294-308 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘cont_mixture.Rmd’ ‘workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GeneralizedModels_legacy.Rmd’ using rmarkdown
--- finished re-building ‘GeneralizedModels_legacy.Rmd’

--- re-building ‘Intro_legacy.Rmd’ using rmarkdown
Quitting from lines 171-174 (Intro_legacy.Rmd) 
Error: processing vignette 'Intro_legacy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_legacy.Rmd’

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

--- re-building ‘simulation_arguments.Rmd’ using rmarkdown
Quitting from lines 111-116 (simulation_arguments.Rmd) 
Error: processing vignette 'simulation_arguments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulation_arguments.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘Intro_legacy.Rmd’ ‘simulation_arguments.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mon
> ### Title: Plot Methods for 'simmer' Monitoring Statistics
> ### Aliases: plot.mon plot.arrivals plot.attributes plot.resources
> 
> ### ** Examples
> 
> t0 <- trajectory("my trajectory") %>%
+   ## add an intake activity
+   seize("nurse", 1) %>%
+   timeout(function() rnorm(1, 15)) %>%
+   release("nurse", 1) %>%
+   ## add a consultation activity
+   seize("doctor", 1) %>%
+   timeout(function() rnorm(1, 20)) %>%
+   release("doctor", 1) %>%
+   ## add a planning activity
+   seize("administration", 1) %>%
+   timeout(function() rnorm(1, 5)) %>%
+   release("administration", 1)
> 
> env <- simmer("SuperDuperSim") %>%
+   add_resource("nurse", 1) %>%
+   add_resource("doctor", 2) %>%
+   add_resource("administration", 1) %>%
+   add_generator("patient", t0, function() rnorm(1, 10, 2)) %>%
+   run(until=80)
> 
> resources <- get_mon_resources(env)
> arrivals <- get_mon_arrivals(env)
> 
> plot(resources, metric="usage", "doctor", items = "server", steps = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot.simmer.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'simmer.plot'

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

    get_mon_arrivals, get_mon_attributes, get_mon_resources

Quitting from lines 72-76 (plot.simmer.Rmd) 
Error: processing vignette 'plot.simmer.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plot.simmer.Rmd’

--- re-building ‘plot.trajectory.Rmd’ using rmarkdown
--- finished re-building ‘plot.trajectory.Rmd’

SUMMARY: processing the following file failed:
  ‘plot.simmer.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.simmr_input
> ### Title: Plot the 'simmr_input' data created from 'simmr_load'
> ### Aliases: plot.simmr_input
> 
> ### ** Examples
> 
> # A simple example with 10 observations, 4 food sources and 2 tracers
> mix = matrix(c(-10.13, -10.72, -11.39, -11.18, -10.81, -10.7, -10.54, 
+ -10.48, -9.93, -9.37, 11.59, 11.01, 10.59, 10.97, 11.52, 11.89, 
+ 11.73, 10.89, 11.05, 12.3), ncol=2, nrow=10)
> colnames(mix) = c('d13C','d15N')
> s_names=c('Source A','Source B','Source C','Source D')
> s_means = matrix(c(-14, -15.1, -11.03, -14.44, 3.06, 7.05, 13.72, 5.96), ncol=2, nrow=4)
> s_sds = matrix(c(0.48, 0.38, 0.48, 0.43, 0.46, 0.39, 0.42, 0.48), ncol=2, nrow=4)
> c_means = matrix(c(2.63, 1.59, 3.41, 3.04, 3.28, 2.34, 2.14, 2.36), ncol=2, nrow=4)
> c_sds = matrix(c(0.41, 0.44, 0.34, 0.46, 0.46, 0.48, 0.46, 0.66), ncol=2, nrow=4)
> conc = matrix(c(0.02, 0.1, 0.12, 0.04, 0.02, 0.1, 0.09, 0.05), ncol=2, nrow=4)
> 
> simmr_1 = simmr_load(mixtures=mix,
+                      source_names=s_names,
+                      source_means=s_means,
+                      source_sds=s_sds,
+                      correction_means=c_means,
+                      correction_sds=c_sds,
+                      concentration_means = conc)
> 
> # Plot
> plot(simmr_1)
Warning: Ignoring unknown aesthetics: height
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simmr.Rmd’ using rmarkdown
Quitting from lines 122-123 (simmr.Rmd) 
Error: processing vignette 'simmr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simmr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘benefits.Rmd’ using rmarkdown
--- finished re-building ‘benefits.Rmd’

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 107-109 (dist_comp.Rmd) 
Error: processing vignette 'dist_comp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dist_comp.Rmd’

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

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

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

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 208-214 (sixth_validpdf.Rmd) 
Error: processing vignette 'sixth_validpdf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sixth_validpdf.Rmd’

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

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 293-294 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘dist_comp.Rmd’ ‘sixth_validpdf.Rmd’ ‘workflow.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggfitStrata
> ### Title: Graph fitted stratified survival curves from Cox Proportional
> ###   Hazards models
> ### Aliases: ggfitStrata
> 
> ### ** Examples
> 
> # Load packages
> library(survival)
> library(simPH)
> 
> # Subset data
> bladder1 <- bladder[bladder$enum < 5, ]
> 
> # Estimate coxph model (note that this model is for code illustration only)
> M1 <- coxph(Surv(stop, event) ~ (rx + size + number) + strata(enum) +
+                 cluster(id), bladder1)
> 
> # Find predicted values
> M1Fit <- survfit(M1)
> 
> # Plot strata in a grid
> ggfitStrata(M1Fit, byStrata = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggfitStrata ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPH-overview.Rnw’ using knitr
All Xl set to 0.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Quitting from lines 309-319 (simPH-overview.Rnw) 
Error: processing vignette 'simPH-overview.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simPH-overview.Rnw’

SUMMARY: processing the following file failed:
  ‘simPH-overview.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Corr_Cont_System.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Loading required package: SimCorrMix
Quitting from lines 378-386 (Corr_Cont_System.Rmd) 
Error: processing vignette 'Corr_Cont_System.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Corr_Cont_System.Rmd’

--- re-building ‘Corr_MultiVarType_System.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Loading required package: SimCorrMix
Quitting from lines 331-339 (Corr_MultiVarType_System.Rmd) 
Error: processing vignette 'Corr_MultiVarType_System.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Corr_MultiVarType_System.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘Corr_Cont_System.Rmd’ ‘Corr_MultiVarType_System.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simstandard_tutorial.Rmd’ using rmarkdown
Quitting from lines 122-124 (simstandard_tutorial.Rmd) 
Error: processing vignette 'simstandard_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simstandard_tutorial.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname="y", dist="uniform", formula="-5;5")
> 
> dt <- genData(1000, def)
> 
> # Define conditions
> 
> defC <- defCondition(condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+                      variance = 1,dist = "normal")
> defC <- defCondition(defC, condition = "x == 2",
+                      formula = "3 - 3*y + y^2", variance = 2, dist="normal")
> defC <- defCondition(defC, condition = "x == 3",
+                      formula = "abs(y)", dist="poisson")
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
> 
> ggplot(data = dt, aes(x=y, y=NewVar, group = x)) +
+   geom_point(aes(color = factor(x)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [56s/61s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Got this Sys.setenv line from https://github.com/luckyrandom/cmaker/blob/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0/tests/testthat.R
  > # so that devtools:check() won't hang.
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(simulator)
  
  Attaching package: 'simulator'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("simulator")
  ── 1. Failure: create makes a template that can be run without error (@test-crea
  any(grepl("error", readLines(a), ignore.case = TRUE)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 125 SKIPPED: 3 FAILED: 1
  1. Failure: create makes a template that can be run without error (@test-create.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘big_crush_test.Rmd’ using rmarkdown
--- finished re-building ‘big_crush_test.Rmd’

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

--- re-building ‘uniform_rng_with_sitmo.Rmd’ using rmarkdown
Quitting from lines 159-163 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette 'uniform_rng_with_sitmo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘uniform_rng_with_sitmo.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ss.cc
> ### Title: Control Charts
> ### Aliases: ss.cc
> 
> ### ** Examples
> 
> ss.cc("mr", ss.data.pb1, CTQ = "pb.humidity")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ss.cc ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SiZer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Arkansas
> ### Title: Time Series of Macroinvertabrates Abundance in the Arkansas
> ###   River.
> ### Aliases: Arkansas
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> 
> data(Arkansas)
> ggplot(Arkansas, aes(x=year, y=sqrt.mayflies)) + 
+    geom_point()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sjPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dist_chisq
> ### Title: Plot chi-squared distributions
> ### Aliases: dist_chisq
> 
> ### ** Examples
> 
> # a simple chi-squared distribution
> # for 6 degrees of freedom
> dist_chisq(deg.f = 6)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: dist_chisq ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘skynet.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 97-101 (skynet.Rmd) 
Error: processing vignette 'skynet.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘skynet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘slim.Rmd’ using rmarkdown
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette 'slim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘slim.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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))
Warning in matrix(data = seq(1, pn), nrow = nr, ncol = nc) :
  data length [5] is not a sub-multiple or multiple of the number of rows [2]
$`0`
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ExpCatViz ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CustomTable.Rmd’ using rmarkdown
--- finished re-building ‘CustomTable.Rmd’

--- re-building ‘SmartEDA.Rmd’ using rmarkdown
Quitting from lines 134-137 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SmartEDA.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SmartProject
> ### Title: SmartProject Class
> ### Aliases: SmartProject
> ### Keywords: data
> 
> ### ** Examples
> 
> # Initialize SmartProject
> yourSmartRstudy <- SmartProject$new()
> 
> # Initialize fleet object
> yourSmartRstudy$createFleet()
> 
> 
> ######################
> ## Environment Data ##
> ######################
> 
> # Locate the example environment asset' file
> envAssetPath <- system.file("extdata/mapAsset.RDS", package = "smartR")
> 
> # Load environment asset' data
> yourSmartRstudy$importEnv(readRDS(envAssetPath))
> 
> # Setup case study' map
> yourSmartRstudy$sampMap$getGooMap()
> yourSmartRstudy$sampMap$setGooGrid()
> yourSmartRstudy$sampMap$setGooBbox()
> yourSmartRstudy$sampMap$setGgDepth()
> yourSmartRstudy$sampMap$setGgBioDF()
> # View case study' grid
> print(yourSmartRstudy$sampMap$gooGrid)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘readme.Rmd’ using rmarkdown
Quitting from lines 119-130 (readme.Rmd) 
Error: processing vignette 'readme.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘readme.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  ── 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘smoof-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.smoof_function
> ### Title: Generate ggplot2 object.
> ### Aliases: autoplot.smoof_function
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Simple 2D contour plot with activated heatmap for the Himmelblau function
> fn = makeHimmelblauFunction()
> print(autoplot(fn))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘smpic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smpic_save
> ### Title: Save a social media sized ggplot
> ### Aliases: smpic_save
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(ggplot2)
> library(smpic)
> 
> p <- ggplot(iris) +
+      geom_point(aes(Petal.Length, Petal.Width, color = Species), show.legend = FALSE) +
+        geom_label(data = summarise_if(group_by(iris, Species), is.numeric, mean),
+                   aes(Petal.Length, Petal.Width, label = Species, color = Species),
+                   show.legend = FALSE) +
+        labs(x = "Petal Length", y = "Petal Width",
+             title = "Look mom, a flower plot!",
+             subtitle = "Yet another iris data set visualization.",
+             caption = "Source: iris") +
+        theme_minimal()
> 
>   smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: smpic_view ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smpic)
  > 
  > test_check("smpic")
  ── 1. Error: (unknown) (@test-functions.R#20)  ─────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent({
         smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2)
     }) at testthat/test-functions.R:20
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2) at testthat/test-functions.R:21
  10: ggplot2::ggsave(filename = filename, dpi = dpi, width = width.calc, height = height.calc, 
         units = "in", plot = p)
  ...
  19: preDraw(x)
  20: preDraw.gTree(x)
  21: pushvpgp(x)
  22: pushgrobvp(x$vp)
  23: pushgrobvp.viewport(x$vp)
  24: pushViewport(vp, recording = FALSE)
  25: lapply(vps, push.vp, recording)
  26: FUN(X[[i]], ...)
  27: push.vp.viewport(X[[i]], ...)
  28: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-functions.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘make_a_social_media_plot.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (make_a_social_media_plot.Rmd) 
Error: processing vignette 'make_a_social_media_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘make_a_social_media_plot.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allocative.efficiency
> ### Title: Allocative efficiency estimation
> ### Aliases: allocative.efficiency
> 
> ### ** Examples
> 
> data(USMacro)
> 
> USMacro <- USMacro[complete.cases(USMacro),]
> 
> #Extract data
> X <- as.matrix(USMacro[,c("K", "L")])
> y <- USMacro$Y
> 
> X.price <- as.matrix(USMacro[,c("K.price", "L.price")])
> y.price <- rep(1e9, nrow(USMacro)) #Price of $1 billion of output is $1 billion
> 
> #Run model
> efficiency.model <- allocative.efficiency(X, y,
+                                          X.price, y.price,
+                                          X.constrained = X,
+                                          model = "br",
+                                          method = "mc")
> 
> #Plot technical/allocative efficiency over time
> library(ggplot2)
> 
> technical.df <- data.frame(Year = USMacro$Year,
+                           Efficiency = efficiency.model$technical.efficiency)
> 
> ggplot(technical.df, aes(Year, Efficiency)) +
+   geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pairwiseSNHT.Rnw’ using knitr
Quitting from lines 114-121 (pairwiseSNHT.Rnw) 
Error: processing vignette 'pairwiseSNHT.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pairwiseSNHT.Rnw’

--- re-building ‘snht.Rnw’ using knitr
Quitting from lines 93-105 (snht.Rnw) 
Error: processing vignette 'snht.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘snht.Rnw’

SUMMARY: processing the following files failed:
  ‘pairwiseSNHT.Rnw’ ‘snht.Rnw’

Error: Vignette re-building failed.
Execution halted
sclust: no visible global function definition for ‘var’
snipEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 163-167 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotKinship2
> ### Title: Plot the double kinship matrix
> ### Aliases: histKinship2 imageKinship2 plotKinship2
> 
> ### ** Examples
> 
> # load `kin` kinship matrix from `dat50` data set
> data(dat50)
> kin2 <- 2* kin # double kinship matrix
> 
> plotKinship2(kin2) # equivalent to `imageKinship2(kin2)`
> 
> plotKinship2(kin2, "hist") # equivalent to `histKinship2(kin2)`
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sophisthse_intro.Rmd’ using rmarkdown
Quitting from lines 42-44 (sophisthse_intro.Rmd) 
Error: processing vignette 'sophisthse_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sophisthse_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sorvi_tutorial.Rmd’ using rmarkdown
sorvi - Tools for Finnish Open Data.
Copyright (C) 2010-2015 Leo Lahti, Juuso Parkkinen, Juuso Haapanen, Einari Happonen, Jussi Paananen, Joona Lehtomaki ym.

http://github.com/ropengov/sorvi 

 Hard sciences are successful because they deal with soft problems; 
 soft sciences are struggling because they deal with hard problems.
-                        Von Foerster

Computing boostrapped smoothers ...
convert bootstrapped spaghettis to long format
Computing density estimates for each vertical cut ...
vertical cross-sectional density estimate
Tile approach
Build ggplot figure ...
Quitting from lines 241-245 (sorvi_tutorial.Rmd) 
Error: processing vignette 'sorvi_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sorvi_tutorial.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using knitr
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Retrieving indicator 10013
Quitting from lines 99-114 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easyLookSource
> ### Title: Easy look results
> ### Aliases: easyLookSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> n.primary<-length(lapply(results.all,function(x) x$primarySet))
> 
> # show only genes that appear in at least one of the source sets of the investigated pathways
> easyLookSource(sourceObj=results.all, maxnum.variable = n.primary,
+                label.variable = "Genes",label.graph = "Pathways")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
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, 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: 1.65 secs
Quitting from lines 311-312 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sparseMVN.Rnw’ using knitr
Quitting from lines 627-643 (sparseMVN.Rnw) 
Error: processing vignette 'sparseMVN.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sparseMVN.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using.Rmd’ using rmarkdown
Quitting from lines 54-55 (using.Rmd) 
Error: processing vignette 'using.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘spartan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_emulators_and_ensemble
> ### Title: Generate a set of emulators and combine into an ensemble
> ### Aliases: generate_emulators_and_ensemble
> 
> ### ** Examples
> 
> sampleMaxes <- cbind(100,0.9,0.5,0.08,1,5)
> sampleMins <-cbind(0,0.1,0.1,0.015,0.1,0.25)
> modelList <- c("RF","GLM")
> measures<-c("Velocity")
> parameters<-c("stableBindProbability","chemokineExpressionThreshold",
+ "initialChemokineExpressionValue","maxChemokineExpressionValue",
+ "maxProbabilityOfAdhesion","adhesionFactorExpressionSlope")
> data("sim_data_for_emulation")
> partitionedData <- partition_dataset(sim_data_for_emulation[,1:7], parameters,
+ measures, percent_train=75, percent_test=15, percent_validation=10, normalise=TRUE,
+ sample_mins = sampleMins, sample_maxes = sampleMaxes)
> generated_ensemble<-generate_emulators_and_ensemble(modelList, parameters,
+ measures, partitionedData, normalised=TRUE)
[1] "RF"
Velocity ~ stableBindProbability + chemokineExpressionThreshold + 
    initialChemokineExpressionValue + maxChemokineExpressionValue + 
    maxProbabilityOfAdhesion + adhesionFactorExpressionSlope
<environment: 0x557ae1438e68>
Saving 7 x 7 in image
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: generate_emulators_and_ensemble ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SpatialBall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DefShotSeasonGraphTeam
> ### Title: Generates an defensive shot chart for a given team
> ### Aliases: DefShotSeasonGraphTeam
> 
> ### ** Examples
> 
> data("season2017")
> #Examples with several teams
> DefShotSeasonGraphTeam(season2017, team = "Sas")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Starting.Rmd’ using rmarkdown
Quitting from lines 52-54 (Starting.Rmd) 
Error: processing vignette 'Starting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Starting.Rmd’

SUMMARY: processing the following file failed:
  ‘Starting.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘spatialwarnings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_indicator
> ### Title: Custom Spatial Early-Warning signals
> ### Aliases: create_indicator custom_indicator
> 
> ### ** Examples
> 
> 
> # Use the maximum patch size as indicator of degradation
> maxpatchsize <- function(mat) { 
+   max(patchsizes(mat))
+ }
> 
> # Create the indicator function
> maxpatch_sews <- create_indicator(maxpatchsize)
> 
> # Then work with this function as if it were a function from the *_sews 
> # family. 
> mp_indic <- maxpatch_sews(forestgap)
> summary(mp_indic)
Spatial Early-Warning: maxpatchsize 

 9 matrices (size: 400x400)

 Mat. # maxpatchsize
      1       146796
      2       128553
      3       107995
      4        48320
      5          322
      6           70
      7           26
      8           10
      9            6

Use as.data.frame() to retrieve values in a convenient form
> 
> ## Not run: 
> ##D  
> ##D # Assess significance and display trends
> ##D mp_test <- indictest(mp_indic, nperm = 49)
> ##D plot(mp_test)
> ## End(Not run)
> 
> 
> 
> # Try spatial coefficient of variation as a spatial EWS. This function can 
> # have arguments. 
> spatial_cv <- function(mat, subsize) { 
+   matc <- coarse_grain(mat, subsize)
+   return( sd(matc) / mean(matc) )
+ }
> 
> # Create indicator function
> cv_sews <- create_indicator(spatial_cv)
> 
> # Compute and display trends
> cv_indic <- cv_sews(serengeti, subsize = 3)
> plot(cv_indic, along = serengeti.rain)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sfbabel.Rmd’ using rmarkdown
--- finished re-building ‘sfbabel.Rmd’

--- re-building ‘spbabel.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: sp
Checking rgeos availability: TRUE
Quitting from lines 116-122 (spbabel.Rmd) 
Error: processing vignette 'spbabel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spbabel.Rmd’

SUMMARY: processing the following file failed:
  ‘spbabel.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spcosa.Rmd’ using rmarkdown
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.3-1 
Quitting from lines 184-185 (spcosa.Rmd) 
Error: processing vignette 'spcosa.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spcosa.Rmd’

SUMMARY: processing the following file failed:
  ‘spcosa.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
--- finished re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 93-105 (speaq2_illustrations.Rmd) 
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following file failed:
  ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dendrogram_plot
> ### Title: Plot dendrogram
> ### Aliases: dendrogram_plot
> ### Keywords: clustering dendrogram hclust
> 
> ### ** Examples
> 
>   ## Example of a dendrogram
>   data(cachexia)
>   hc.result = hierarchical_clustering(cachexia)
>   dendrogram_plot(cachexia, hc.result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘spectacles-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot-Spectra
> ### Title: Plots an object inheriting from the Spectra class
> ### Aliases: plot-Spectra plot plot.Spectra plot,Spectra,ANY-method
> ###   plot.Spectra
> 
> ### ** Examples
> 
> 
> # Loading example data
> data(australia)
> spectra(australia) <- sr_no ~ ... ~ 350:2500
Wavelength range: 350 to 2500 nm
Spectral resolution: 1 nm
> 
> # Default plotting method
> plot(australia[1:5,])
> 
> # Default plot using ggplot2
> plot(australia[1:5,], gg = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Spectrum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Spectrum
> ### Title: Spectrum: Fast Adaptive Spectral Clustering for Single and
> ###   Multi-view Data
> ### Aliases: Spectrum
> 
> ### ** Examples
> 
> res <- Spectrum(brain[[1]][,1:50])
***Spectrum***
detected views: 1
method: 1
kernel: density
calculating kernel 1
done.
combining kernels if > 1 and making KNN graph...
done.
diffusing on tensor graph...
done.
calculating graph laplacian...
getting eigendecomposition of L...
done.
examining eigenvalues to select K...
optimal K: 3
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Spectrum ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
Quitting from lines 49-51 (Spectrum_vignette.Rmd) 
Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Spectrum_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Spectrum_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘spef-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PanelSurv
> ### Title: Create a PanelSurv Object
> ### Aliases: PanelSurv PanelSurv is.PanelSurv
> 
> ### ** Examples
> 
> data(blaTum)
> response <- with(blaTum, PanelSurv(id, time, count))
> is.PanelSurv(response)
[1] TRUE
> plot(response)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spFSR.Rmd’ using rmarkdown
Quitting from lines 299-301 (spFSR.Rmd) 
Error: processing vignette 'spFSR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spFSR.Rmd’

SUMMARY: processing the following file failed:
  ‘spFSR.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘spind-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: covar.plot
> ### Title: Plot wavelet variance/covariance
> ### Aliases: covar.plot
> 
> ### ** Examples
> 
> data(carlinadata)
> coords <- carlinadata[,4:5]
> 
> covariance <- covar.plot(carlina.horrida ~ aridity + land.use - 1,
+                          data = carlinadata,
+                          coord = coords,
+                          wavelet = "d4",
+                          wtrafo = 'modwt',
+                          plot = 'covar')
> 
> covariance$plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spind_vignette.Rmd’ using rmarkdown
Quitting from lines 51-76 (spind_vignette.Rmd) 
Error: processing vignette 'spind_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spind_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘spind_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘splinetree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotNode
> ### Title: Plot the predicted trajectory for a single node
> ### Aliases: plotNode
> 
> ### ** Examples
> 
> plotNode(tree, 6, includeData=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DPsplithalf-vignette.Rmd’ using rmarkdown
Quitting from lines 207-213 (DPsplithalf-vignette.Rmd) 
Error: processing vignette 'DPsplithalf-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DPsplithalf-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘DPsplithalf-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  ── 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sport_in_r.Rmd’ using rmarkdown
r is missing and will set to default=1500
rd is missing and will set to default=350
r is missing and will set to default=1500
rd is missing and will set to default=350
sigma is missing and will set to default=0.05
r is missing and will set to default=25
rd is missing and will set to default=8.33333333333333
Quitting from lines 133-135 (sport_in_r.Rmd) 
Error: processing vignette 'sport_in_r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sport_in_r.Rmd’

SUMMARY: processing the following file failed:
  ‘sport_in_r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spreadr_vignette.Rmd’ using rmarkdown
Quitting from lines 79-88 (spreadr_vignette.Rmd) 
Error: processing vignette 'spreadr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spreadr_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘spreadr_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sprm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biplot.prm
> ### Title: Biplot for prm objects
> ### Aliases: biplot.prm
> 
> ### ** Examples
> 
> set.seed(5023)
> U <- c(rep(3,20), rep(4,30))
> X <- replicate(6, U+rnorm(50))
> beta <- c(rep(1, 3), rep(-1,3))
> e <- c(rnorm(45,0,1.5),rnorm(5,-20,1))
> y <- X%*%beta + e
> d <- as.data.frame(X)
> d$y <- y
> mod <- prms(y~., data=d, a=2, fun="Hampel")
> biplot(mod, comps = c(1, 2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: biplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SPUTNIK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binKmeans,msi.dataset-method
> ### Title: Return a binary mask generated applying k-means clustering on
> ###   peaks intensities.
> ### Aliases: binKmeans,msi.dataset-method binKmeans
> 
> ### ** Examples
> 
> ## Load package
> library("SPUTNIK")
> 
> ## Create the msi.dataset-class object
> sz <- c(5, 4)
> x <- matrix(rnorm(sz[1] * sz[2] * 20), sz[1]*sz[2], 20)
> mz <- sort(sample(100, ncol(x)))
> msiX <- msiDataset(x, mz, sz[1], sz[2])
> 
> ## Binarize the reference image
> refBin <- binKmeans(msiX)
> 
> ## Plot the binarized reference
> plot(refBin)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-srvyr.Rmd’ using rmarkdown
--- finished re-building ‘extending-srvyr.Rmd’

--- re-building ‘srvyr-database.Rmd’ using rmarkdown
--- finished re-building ‘srvyr-database.Rmd’

--- re-building ‘srvyr-vs-survey.Rmd’ using rmarkdown
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart


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 31-47 (srvyr-vs-survey.Rmd) 
Error: processing vignette 'srvyr-vs-survey.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘srvyr-vs-survey.Rmd’

SUMMARY: processing the following file failed:
  ‘srvyr-vs-survey.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ss3sim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_scalar_boxplot
> ### Title: Print scalar values as boxplots.
> ### Aliases: plot_scalar_boxplot
> 
> ### ** Examples
> 
> scalar_dat$depletion <- with(scalar_dat,
+   (depletion_om - depletion_em) / depletion_om)
> plot_scalar_boxplot(scalar_dat, x = "E", y = "depletion", horiz = "D",
+   relative.error = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_scalar_boxplot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 680-688 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘making-functions.Rmd’ using rmarkdown
--- finished re-building ‘making-functions.Rmd’

--- re-building ‘making-models.Rmd’ using rmarkdown
--- finished re-building ‘making-models.Rmd’

--- re-building ‘modifying-models.Rmd’ using rmarkdown
--- finished re-building ‘modifying-models.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ssdtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.fitdist
> ### Title: Autoplot
> ### Aliases: autoplot.fitdist
> 
> ### ** Examples
> 
> ggplot2::autoplot(boron_lnorm)
Warning: Removed 98 rows containing missing values (geom_path).
geom_path: Each group consists of only one observation. Do you need to adjust
the group aesthetic?
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ssdtools-manual.Rmd’ using rmarkdown
Quitting from lines 115-119 (ssdtools-manual.Rmd) 
Error: processing vignette 'ssdtools-manual.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ssdtools-manual.Rmd’

SUMMARY: processing the following file failed:
  ‘ssdtools-manual.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Running examples in ‘sssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary_vcf
> ### Title: VCF Data Summary
> ### Aliases: summary_vcf
> 
> ### ** Examples
> 
> data("vcf_example")
> tmp <- summary_vcf(vcf = vcf_example, ZG = 'het', CHR = c(1,2))
> plot(tmp$scatter)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stability-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ammi_biplot
> ### Title: Additive Main Effects and Multiplicative Interaction (AMMI)
> ###   Biplot
> ### Aliases: ammi_biplot ammi_biplot.default
> 
> ### ** Examples
> 
> 
> data(ge_data)
>      ammi_biplot(
+             .data = ge_data
+           , .y    = Yield
+           , .rep  = Rep
+           , .gen  = Gen
+           , .env  = Env
+       )
$aami.biplot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stabm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotFeatures
> ### Title: Plot Selected Features
> ### Aliases: plotFeatures
> 
> ### ** Examples
> 
> feats = list(1:3, 1:4, 1:5)
> mat = 0.92 ^ abs(outer(1:10, 1:10, "-"))
> plotFeatures(features = feats)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotFeatures ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stacomiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report_df-class
> ### Title: Report on fishway operation
> ### Aliases: report_df-class report_df
> ### Keywords: classes
> 
> ### ** Examples
> 
> require(stacomiR)
> stacomi(gr_interface=FALSE,
+ 	login_window=FALSE,
+ 	database_expected=FALSE)
> ## An example that will work with the database installed only
> ## Not run: 
> ##D   r_df=new("report_df")
> ##D   r_df<-choice_c(r_df,
> ##D 	  1,
> ##D 	  horodatedebut="2015-01-01",
> ##D 	  horodatefin="2015-12-31",
> ##D 	  silent=TRUE)
> ##D   Sys.setenv(TZ='GMT')
> ##D   # the times at Arzal are recorded continuously
> ##D   # they are converted to date when a time appears while the hour is changing
> ##D   # hence the following
> ##D   r_df<-connect(r_df)
> ## End(Not run)
> 
> data("r_df")
> plot(r_df,plot.type="4")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 308-310 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘staRdom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eem_extend2largest
> ### Title: EEM sample data is extended to include all wavelengths in all
> ###   samples
> ### Aliases: eem_extend2largest
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> data(eem_list)
> eem_list <- eem_exclude(eem_list[1:5] %>%
+ `class<-`("eemlist"), exclude = list(em = c(318,322,326,550,438), ex = c(270,275))) %>%
+ eem_bind(eem_list[6:15] %>% `class<-`("eemlist"))
> ggeem(eem_list)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_analysis_of_DOM_samples.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Writing 21 Bibtex entries ... OK
Results written to file 'references.bib'
--- finished re-building ‘Basic_analysis_of_DOM_samples.Rmd’

--- re-building ‘PARAFAC_analysis_of_EEM.Rmd’ using rmarkdown

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 151-152 (PARAFAC_analysis_of_EEM.Rmd) 
Error: processing vignette 'PARAFAC_analysis_of_EEM.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PARAFAC_analysis_of_EEM.Rmd’

SUMMARY: processing the following file failed:
  ‘PARAFAC_analysis_of_EEM.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘starma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stacf
> ### Title: Space-time autocorrelation functions
> ### Aliases: stacf stpacf
> ### Keywords: starma identification diagnostic acf stacf pacf stpacf
> 
> ### ** Examples
> 
> data(nb_mat)	# Get neighbourhood matrices
> 
> # Simulate a STARMA model
> eps <- matrix(rnorm(94*200), 200, 94)
> sim <- eps
> for (t in 3:200) {
+ 	sim[t,] <- (.4*blist[[1]] + .25*blist[[2]]) %*% sim[t-1,] +
+ 		(.25*blist[[1]]                ) %*% sim[t-2,] +
+ 		(            - .3*blist[[2]]) %*% eps[t-1,] +
+ 		eps[t, ]
+ }
> 
> sim <- sim[101:200,]
> sim <- stcenter(sim)	# Center and scale the dataset
> 
> # Plot stacf and stpacf
> stacf(sim, blist)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: stacf ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘starmie-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bestK
> ### Title: Determine a suitable K value from multiple Structure runs
> ### Aliases: bestK
> 
> ### ** Examples
> 
> multi_K <- exampleStructure("multiple_runs")
> # Run the evanno method and display diagnostic plots.
> evanno_results <- bestK(multi_K, method = "evanno")
Creating diagnostic plots for structure runs.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: bestK -> bestK.structList -> bestK_evanno
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-starmie-admixture.Rmd’ using rmarkdown
Quitting from lines 71-72 (using-starmie-admixture.Rmd) 
Error: processing vignette 'using-starmie-admixture.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-starmie-admixture.Rmd’

--- re-building ‘using-starmie.Rmd’ using rmarkdown
Quitting from lines 112-113 (using-starmie.Rmd) 
Error: processing vignette 'using-starmie.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-starmie.Rmd’

SUMMARY: processing the following files failed:
  ‘using-starmie-admixture.Rmd’ ‘using-starmie.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stars
> ### Title: ggplot geom for stars objects
> ### Aliases: geom_stars
> 
> ### ** Examples
> 
> system.file("tif/L7_ETMs.tif", package = "stars") %>% read_stars() -> x
> library(ggplot2)
> ggplot() + geom_stars(data = x) +
+     coord_equal() +
+     facet_wrap(~band) +
+     theme_void() +
+     scale_x_discrete(expand=c(0,0))+
+     scale_y_discrete(expand=c(0,0))
Error in Summary.unit(c(0, 0), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stars1.Rmd’ using rmarkdown
--- finished re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
Quitting from lines 105-115 (stars3.Rmd) 
Error: processing vignette 'stars3.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
--- finished re-building ‘stars5.Rmd’

SUMMARY: processing the following file failed:
  ‘stars3.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_binmean
> ### Title: Plot the mean of y over the mean of x within bins of x.
> ### Aliases: stat_binmean
> 
> ### ** Examples
> 
> library(ggplot2)
> g <- ggplot(iris, aes(x = Sepal.Width , y = Sepal.Length)) 
> g + stat_binmean(n = 10)
Warning: Computation failed in `stat_binmean()`:
could not find function "ntile"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘states-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: id_date_sequence
> ### Title: Identify date sequences
> ### Aliases: id_date_sequence
> 
> ### ** Examples
> 
> library("ggplot2")
> d1 <- as.Date("2018-01-01")
> d2 <- as.Date("2025-01-01")
> seq1 <- seq(d1, d2, by = "year")
> data.frame(seq1, id=id_date_sequence(seq1, "year"))
        seq1 id
1 2018-01-01  1
2 2019-01-01  1
3 2020-01-01  1
4 2021-01-01  1
5 2022-01-01  1
6 2023-01-01  1
7 2024-01-01  1
8 2025-01-01  1
> # With a gap, should be two ids
> df <- data.frame(date = seq1[-4], id=id_date_sequence(seq1[-4], "year"), cowcode = 999)
> df
        date id cowcode
1 2018-01-01  1     999
2 2019-01-01  1     999
3 2020-01-01  1     999
4 2022-01-01  2     999
5 2023-01-01  2     999
6 2024-01-01  2     999
7 2025-01-01  2     999
> 
> # The point is to plot countries with interrupted independence correctly:
> df$y <- c(rep(1, 3), rep(2, 4))
> df$id <- paste0(df$cowcode, df$id)
> df
        date   id cowcode y
1 2018-01-01 9991     999 1
2 2019-01-01 9991     999 1
3 2020-01-01 9991     999 1
4 2022-01-01 9992     999 2
5 2023-01-01 9992     999 2
6 2024-01-01 9992     999 2
7 2025-01-01 9992     999 2
> ggplot(df, aes(x = date, y = y, group = cowcode)) + geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘StatRank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Visualization.Empirical
> ### Title: RPD Visualization
> ### Aliases: Visualization.Empirical
> 
> ### ** Examples
> 
> library(ggplot2)
> library(gridExtra)
> data(Data.Test)
> Visualization.Empirical(Data.Test, 0.5)
Warning: Removed 1 rows containing missing values (position_stack).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Visualization.Empirical ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Get_started_with_statsDK.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

The following object is masked from 'package:base':

    date

Tables collected succesfully
Quitting from lines 109-120 (Get_started_with_statsDK.Rmd) 
Error: processing vignette 'Get_started_with_statsDK.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Get_started_with_statsDK.Rmd’

SUMMARY: processing the following file failed:
  ‘Get_started_with_statsDK.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘statsr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stminsights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_effects
> ### Title: extract stm effect estimates
> ### Aliases: get_effects
> 
> ### ** Examples
> 
> 
> library(stm)
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(ggplot2)
> 
> # store effects
> prep <- estimateEffect(1:3 ~ treatment + pid_rep, gadarianFit, gadarian)
> 
> effects <- get_effects(estimates = prep,
+                       variable = 'treatment',
+                       type = 'pointestimate')
> 
> 
> # plot effects
> effects %>% filter(topic == 3) %>%
+ ggplot(aes(x = value, y = proportion)) +
+  geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.1, size = 1) +
+  coord_flip() + theme_light() + labs(x = 'Treatment', y = 'Topic Proportion')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘STMotif-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: displayPlotSeries
> ### Title: Plot spatial series by selected columns
> ### Aliases: displayPlotSeries
> 
> ### ** Examples
> 
> #Launch all the workflow
> #Plot the result
> D  <- STMotif::example_dataset
> DS <- NormSAX(STMotif::example_dataset,7)
> stmotifs <- SearchSTMotifs(D,DS,3,7,10,10,3,7)
> rstmotifs <- RankSTMotifs(stmotifs)
> displayPlotSeries(dataset = D, rmotifs = rstmotifs ,position = 1 ,space = c(1,2,5:7))
Error in Summary.unit(c(4, 4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘discovery-motifs.Rmd’ using rmarkdown
--- finished re-building ‘discovery-motifs.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 84-86 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

--- re-building ‘normalization-and-sax.Rmd’ using rmarkdown
--- finished re-building ‘normalization-and-sax.Rmd’

--- re-building ‘search-stmotifs.Rmd’ using rmarkdown
--- finished re-building ‘search-stmotifs.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Details.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Quitting from lines 237-261 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Details.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 77-78 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Details.Rmd’ ‘Overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘stpp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rinfec
> ### Title: Generate infection point patterns
> ### Aliases: rinfec
> 
> ### ** Examples
> 
> # inhibition; spatial distribution: uniform
> inf1 = rinfec(npoints=100, alpha=0.2, beta=0.6, gamma=0.5,
+ maxrad=c(0.075,0.5), t.region=c(0,50), s.distr="uniform", 
+ t.distr="uniform", h="gaussian", p="min", recent="all", t0=0.02, 
+ inhibition=TRUE)
> plot(inf1$xyt, style="elegant")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘strataG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sequenceLikelihoods
> ### Title: Sequence Likelihoods
> ### Aliases: sequenceLikelihoods
> 
> ### ** Examples
> 
> library(ape)
> data(dolph.haps)
> 
> sequenceLikelihoods(as.DNAbin(dolph.haps))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sequenceLikelihoods ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘StratigrapheR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fastPairs
> ### Title: Scatterplot Matrices for large dataset
> ### Aliases: fastPairs
> 
> ### ** Examples
> 
> fastPairs(iris[1:4],bins=10)
Error in Summary.unit(c(4.8, 4.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘STraTUS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw.fully.sampled
> ### Title: For a sample with no unsampled hosts, draw the annotated
> ###   phylogeny using 'ggtree'
> ### Aliases: draw.fully.sampled
> 
> ### ** Examples
> 
> generator <- tt.generator(stratus.example.tree)
> samples <- sample.tt(generator, 1)
> draw.fully.sampled(generator, samples[[1]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stripless-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.structured
> ### Title: Methods for structured objects.
> ### Aliases: plot.structured print.structured print.summary.structured
> ###   summary.structured
> 
> ### ** Examples
> 
> require(datasets)
> # quakes data
> #
> # Create and save plot
> out <- strucplot(lat ~ long|cut(mag,5)*cut(depth,4), data = quakes,
+   col="blue", main = "Earthquake locations, by magnitude and depth")
> 
> # Summary:
> summary(out)

  xyplot call:
xyplot(lat ~ long | cut(mag, 5) * cut(depth, 4), data = quakes, 
    col = "blue", main = "Earthquake locations, by magnitude and depth")

 Actual formula:
NULL

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

> 
> # Default output -- structure legend on console only
>    print(out)

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

> 
> # Add legends to the plot on either right or bottom (note partial matching)
>    print(out, legendLoc = "right")

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

Error in matchData[[i]] * amount[i] : 
  non-numeric argument to binary operator
Calls: print ... <Anonymous> -> widthDetails -> widthDetails.frame -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘StructFDR.Rmd’ using rmarkdown
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette 'StructFDR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘StructFDR.Rmd’

SUMMARY: processing the following file failed:
  ‘StructFDR.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/subprocess.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotting_functions.Rmd’ using rmarkdown
trying URL ‘https://www.imbi.uni-freiburg.de/imbi/Royston-Sauerbrei-book/Multivariable_Model-building/downloads/datasets/adv_prostate_ca.zip’
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

Quitting from lines 73-74 (plotting_functions.Rmd) 
Error: processing vignette 'plotting_functions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotting_functions.Rmd’

--- re-building ‘subbuild_function.Rmd’ using rmarkdown
trying URL ‘https://www.imbi.uni-freiburg.de/imbi/Royston-Sauerbrei-book/Multivariable_Model-building/downloads/datasets/adv_prostate_ca.zip’
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

--- finished re-building ‘subbuild_function.Rmd’

--- re-building ‘subtee_package.Rmd’ using rmarkdown
trying URL ‘https://www.imbi.uni-freiburg.de/imbi/Royston-Sauerbrei-book/Multivariable_Model-building/downloads/datasets/adv_prostate_ca.zip’
Content type 'application/zip' length 62590 bytes (61 KB)
==================================================
downloaded 61 KB

--- finished re-building ‘subtee_package.Rmd’

SUMMARY: processing the following file failed:
  ‘plotting_functions.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sugrrants-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: frame_calendar
> ### Title: Rearrange a temporal data frame to a calendar-based data format
> ###   using linear algebra
> ### Aliases: frame_calendar prettify
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> # compute the calendar layout for the data frame
> calendar_df <- pedestrian %>%
+   filter(Sensor_ID == 13, Year == 2016) %>%
+   frame_calendar(x = Time, y = Hourly_Counts, date = Date, nrow = 4)
> 
> # ggplot
> p1 <- calendar_df %>%
+   ggplot(aes(x = .Time, y = .Hourly_Counts, group = Date)) +
+   geom_line()
> prettify(p1, size = 3, label.padding = unit(0.15, "lines"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘frame-calendar.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: viridisLite
Loading required package: ggplot2
Quitting from lines 52-56 (frame-calendar.Rmd) 
Error: processing vignette 'frame-calendar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘frame-calendar.Rmd’

SUMMARY: processing the following file failed:
  ‘frame-calendar.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘summariser-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary_plot
> ### Title: summary_plot
> ### Aliases: summary_plot
> 
> ### ** Examples
> 
> data(iris)
> sum1 <- summary_stats(iris, measure = "Sepal.Length", Species)
> summary_plot(sum1, x="Species", colour="Species")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘superheat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: superheat
> ### Title: Generate supervised heatmaps.
> ### Aliases: superheat
> 
> ### ** Examples
> 
> # plot a heatmap of the numerical iris variables
> # cluster by species and plot Sepal.Length on the right
> # save the superheat object to access the membership vectors
> sh <- superheat(X = iris[,-c(1, 5)],
+                 yr = iris[,1],
+                 yr.axis.name = "Sepal.Length",
+                 membership.rows = iris$Species)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: superheat ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Guide-to-SuperLearner.Rmd’ using rmarkdown
Quitting from lines 191-213 (Guide-to-SuperLearner.Rmd) 
Error: processing vignette 'Guide-to-SuperLearner.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Guide-to-SuperLearner.Rmd’

--- re-building ‘SuperLearnerPresent.Rnw’ using Sweave
--- finished re-building ‘SuperLearnerPresent.Rnw’

SUMMARY: processing the following file failed:
  ‘Guide-to-SuperLearner.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘SurvBoost-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.boosting
> ### Title: Boosting plot function
> ### Aliases: plot.boosting
> ### Keywords: boosting gradient
> 
> ### ** Examples
> 
> data <- simulate_survival_cox(true_beta=c(1,1,1,1,1,0,0,0,0,0))
> formula <- as.formula("Surv(time,delta) ~ strata(strata_idx) + V1 + V2 + 
+ V3 + V4 + V5 + V6 + V7 + V8 + V9 + V10" )
> boosting.output <- boosting_core(formula, data, rate=0.1, control=500)
> plot.boosting(boosting.output)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘surveillance-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sts_ggplot
> ### Title: Time-Series Plots for '"sts"' Objects Using 'ggplot2'
> ### Aliases: autoplot.sts
> ### Keywords: hplot ts
> 
> ### ** Examples
> 
> ## compare traditional plot() with ggplot2-based autoplot.sts()
> if (requireNamespace("ggplot2")) {
+     data("measlesDE")
+     plot(measlesDE)
+     autoplot.sts(measlesDE)
+ }
Loading required namespace: ggplot2
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘survey-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: svyplot
> ### Title: Plots for survey data
> ### Aliases: svyplot svyplot.default
> ### Keywords: survey hplot
> 
> ### ** Examples
> 
> data(api)
> dstrat<-svydesign(id=~1,strata=~stype, weights=~pw, data=apistrat, fpc=~fpc)
> 
> svyplot(api00~api99, design=dstrat, style="bubble")
> svyplot(api00~api99, design=dstrat, style="transparent",pch=19)
> 
> ## these two require the hexbin package 
> svyplot(api00~api99, design=dstrat, style="hex", xlab="1999 API",ylab="2000 API")
Error in (function (cl, name, valueClass)  : 
  c("assignment of an object of class “simpleUnit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE", "assignment of an object of class “unit” is not valid for @‘mar’ in an object of class “hexVP”; is(value, \"unit\") is not TRUE")
Calls: svyplot ... svyplot.default -> <Anonymous> -> hexViewport -> <Anonymous>
Execution halted
Running examples in ‘surveysd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.surveysd
> ### Title: Plot surveysd-Objects
> ### Aliases: plot.surveysd
> 
> ### ** Examples
> 
> 
> library(surveysd)
> library(laeken)
> library(data.table)
> 
> eusilc <- demo.eusilc(n = 4, prettyNames = TRUE)
> 
> dat_boot <- draw.bootstrap(eusilc, REP = 3, hid = "hid", weights = "pWeight",
+                            strata = "region", period = "year")
> 
> # calibrate weight for bootstrap replicates
> dat_boot_calib <- recalib(dat_boot, conP.var = "gender", conH.var = "region")
Convergence reached in 2 steps 

Convergence reached in 2 steps 

Convergence reached in 3 steps 

> 
> # estimate weightedRatio for povmd60 per period
> group <- list("gender", "region", c("gender", "region"))
> err.est <- calc.stError(dat_boot_calib, var = "povertyRisk", fun = weightedRatio,
+                         group = group , period.mean = NULL)
> 
> 
> plot(err.est)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multivariate.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 88-89 (multivariate.Rmd) 
Error: processing vignette 'multivariate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘multivariate.Rmd’

--- re-building ‘univariate.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 104-105 (univariate.Rmd) 
Error: processing vignette 'univariate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘univariate.Rmd’

SUMMARY: processing the following files failed:
  ‘multivariate.Rmd’ ‘univariate.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘survminer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BMT
> ### Title: Bone Marrow Transplant
> ### Aliases: BMT
> 
> ### ** Examples
> 
> data(BMT)
> 
> # Data preparaion
> #+++++++++++++++++++++
> # Label diseases
> BMT$dis <- factor(BMT$dis, levels = c(0,1),
+    labels = c("ALL", "AML"))
> # Label status
> BMT$status <- factor(BMT$status, levels = c(0,1,2),
+   labels = c("Censored","Mortality","Relapse"))
> 
> # Cumulative Incidence Function
> # ++++++++++++++++++++++++++
> fit <- cmprsk::cuminc(
+   ftime = BMT$ftime,      # Failure time variable
+   fstatus = BMT$status,   # Codes for different causes of failure
+   group = BMT$dis         # Estimates will calculated within groups
+  )
> 
> # Visualize
> # +++++++++++++++++++++++
> ggcompetingrisks(fit)
Error in Summary.unit(c(4.8, 4.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Informative_Survival_Plots.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Quitting from lines 67-73 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Informative_Survival_Plots.Rmd’

--- re-building ‘Playing_with_fonts_and_texts.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Quitting from lines 45-50 (Playing_with_fonts_and_texts.Rmd) 
Error: processing vignette 'Playing_with_fonts_and_texts.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Playing_with_fonts_and_texts.Rmd’

--- re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Quitting from lines 98-99 (Specifiying_weights_in_log-rank_comparisons.Rmd) 
Error: processing vignette 'Specifiying_weights_in_log-rank_comparisons.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Specifiying_weights_in_log-rank_comparisons.Rmd’

SUMMARY: processing the following files failed:
  ‘Informative_Survival_Plots.Rmd’ ‘Playing_with_fonts_and_texts.Rmd’
  ‘Specifiying_weights_in_log-rank_comparisons.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘survtmle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘survtmle_intro.Rmd’ using rmarkdown
Quitting from lines 541-543 (survtmle_intro.Rmd) 
Error: processing vignette 'survtmle_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘survtmle_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘survtmle_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sValues-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sValues
> ### Title: Plot method for S-values
> ### Aliases: plot.sValues
> 
> ### ** Examples
> 
> # growth regressions example
> data(economic_growth)
> eg_sv <- sValues(GR6096 ~ ., data = economic_growth)
> plot(eg_sv, R2_bounds = c(0.5, 1))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sValues.Rnw’ using knitr
Quitting from lines 148-149 (sValues.Rnw) 
Error: processing vignette 'sValues.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sValues.Rnw’

SUMMARY: processing the following file failed:
  ‘sValues.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘svars-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: id.dc
> ### Title: Independence-based identification of SVAR models based on
> ###   distance covariances
> ### Aliases: id.dc
> 
> ### ** Examples
> 
> 
> # data contains quarterly observations from 1965Q1 to 2008Q3
> # x = output gap
> # pi = inflation
> # i = interest rates
> set.seed(23211)
> v1 <- vars::VAR(USA, lag.max = 10, ic = "AIC" )
> x1 <- id.dc(v1)
> summary(x1)

Identification Results
---------------------- 

Method: Distance covariances
Sample size: 169

Estimated B Matrix (unique decomposition of the covariance matrix): 
          [,1]        [,2]      [,3]
x  0.541926899 -0.36707854 0.1964223
pi 0.508827712  0.92428628 0.1967426
i  0.003560267  0.02576151 0.8194037
> 
> # switching columns according to sign pattern
> x1$B <- x1$B[,c(3,2,1)]
> x1$B[,3] <- x1$B[,3]*(-1)
> 
> # impulse response analysis
> i1 <- irf(x1, n.ahead = 30)
> plot(i1, scales = 'free_y')
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘SVMMaj-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.svmmaj
> ### Title: Out-of-Sample Prediction from Unseen Data.
> ### Aliases: predict.svmmaj
> 
> ### ** Examples
> 
> 
> attach(AusCredit)
> 
> ## model training
> model <- svmmaj(X[1:400, ], y[1:400], hinge = 'quadratic', lambda = 1)
> ## model prediction
> q4     <- predict(model, X[-(1:400), ], y[-(1:400)], show.plot = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: predict ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘paper.Rnw’ using Sweave
Error: processing vignette 'paper.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘paper.Rnw’

SUMMARY: processing the following file failed:
  ‘paper.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘swfscMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotAssignments
> ### Title: Plot assignment distributions
> ### Aliases: plotAssignments
> 
> ### ** Examples
> 
> n <- 40
> probs <- abs(c(rnorm(n, 80, 10), rnorm(n, 20, 10)))
> probs <- (probs - min(probs)) / max(probs)
> probs <- cbind(probs, 1 - probs)
> colnames(probs) <- NULL
> orig <- rep(c("Group.1", "Group.2"), each = n)
> 
> plotAssignments(probs, orig)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotAssignments ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘synthpop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare.fit.synds
> ### Title: Compare model estimates based on synthesised and observed data
> ### Aliases: compare.fit.synds print.compare.fit.synds
> 
> ### ** Examples
> 
> ods <- SD2011[,c("sex","age","edu","smoke")]
> s1 <- syn(ods, m = 3)
Synthesis number 1
--------------------
 sex age edu smoke
Synthesis number 2
--------------------
 sex age edu smoke
Synthesis number 3
--------------------
 sex age edu smoke
> f1 <- glm.synds(smoke ~ sex + age + edu, data = s1, family = "binomial")
> compare(f1, ods) 

Call used to fit models to the data:
glm.synds(formula = smoke ~ sex + age + edu, family = "binomial", 
    data = s1)

Differences between results based on synthetic and observed data:
                            Std. coef diff p value CI overlap
(Intercept)                     0.18476889   0.749  0.9528642
sexFEMALE                      -2.77459296   0.000  0.2921827
age                             0.02830647   0.961  0.9927788
eduVOCATIONAL/GRAMMAR           0.68904229   0.233  0.8242207
eduSECONDARY                   -0.05753616   0.921  0.9853221
eduPOST-SECONDARY OR HIGHER     0.10597022   0.854  0.9729663

Measures for 3 syntheses and 6 coefficients
Mean confidence interval overlap:  0.8367225
Mean absolute std. coef diff:  0.6400362
Lack-of-fit: 32.15351; p-value 0 for test that synthesis model is compatible 
with a chi-squared test with 6 degrees of freedom

Confidence interval plot:
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘inference.Rnw’ using Sweave
Loading required package: lattice
Loading required package: MASS
Loading required package: nnet
Loading required package: ggplot2
Error: processing vignette 'inference.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'inference.Rnw'

--- re-building ‘synthpop.Rnw’ using Sweave
Loading required package: lattice
Loading required package: MASS
Loading required package: nnet
Loading required package: ggplot2
Error: processing vignette 'synthpop.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'synthpop.Rnw'

SUMMARY: processing the following files failed:
  ‘inference.Rnw’ ‘synthpop.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sysid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arx
> ### Title: Estimate ARX Models
> ### Aliases: arx
> 
> ### ** Examples
> 
> data(arxsim)
> mod_arx <- arx(arxsim,c(1,2,2))
> mod_arx
Discrete-time ARX model: A(z)y[k] = B(z)u[k] +  e[k] 

A(q^{-1}) = 1	- 0.5241 (+/- 0.0316) q^{-1}	
B(q^{-1}) = 0.5875 (+/- 0.0123) q^{-2}	- 0.2238 (+/- 0.0221) q^{-3}	


 Fit Characteristics 
     MSE    FPE FitPer  AIC  AICc    nAIC  BIC
1 0.3876 0.3885     50 4835 45.49 -0.9455 4852
> plot(mod_arx) # plot the predicted and actual responses
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tabula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMatrix
> ### Title: Matrix plot
> ### Aliases: plotMatrix plotMatrix-method matrigraphe
> ###   plotMatrix,CountMatrix-method plotMatrix,FrequencyMatrix-method
> ###   plotMatrix,IncidenceMatrix-method
> 
> ### ** Examples
> 
> # Abundance data
> ## Coerce dataset to abundance matrix
> ## Data from Desachy 2004
> count <- as(compiegne, "CountMatrix")
> 
> # Plot matrix diagram...
> ## ...without threshod (i.e. heatmap)
> plotMatrix(count)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diversity.Rmd’ using rmarkdown
--- finished re-building ‘diversity.Rmd’

--- re-building ‘tabula.Rmd’ using rmarkdown
Quitting from lines 153-159 (tabula.Rmd) 
Error: processing vignette 'tabula.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tabula.Rmd’

SUMMARY: processing the following file failed:
  ‘tabula.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tadaatoolbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tadaa_balance
> ### Title: Grouping design balance
> ### Aliases: tadaa_balance
> 
> ### ** Examples
> 
> tadaa_balance(ngo, jahrgang, geschl)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tadaatoolbox)
  > 
  > test_check("tadaatoolbox")
  ── 1. Error: tadaa_int produces plot (@test-plots.R#12)  ───────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_length(tadaa_int(ngo, stunzahl, jahrgang, geschl, grid = FALSE, print = TRUE), 
         2) at testthat/test-plots.R:12
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tadaa_int(ngo, stunzahl, jahrgang, geschl, grid = FALSE, print = TRUE)
  5: print(p1)
  6: print.ggplot(p1)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 160 SKIPPED: 1 FAILED: 1
  1. Error: tadaa_int produces plot (@test-plots.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 137-142 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

--- re-building ‘test_output.Rmd’ using rmarkdown
--- finished re-building ‘test_output.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_tbrf.Rmd’ using rmarkdown
Quitting from lines 82-95 (intro_to_tbrf.Rmd) 
Error: processing vignette 'intro_to_tbrf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_to_tbrf.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_to_tbrf.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tcgsaseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: voom_weights
> ### Title: Precision weights accounting for heteroscedasticity in RNA-seq
> ###   count data
> ### Aliases: voom_weights
> 
> ### ** Examples
> 
> #rm(list=ls())
> set.seed(123)
> 
> G <- 10000
> n <- 12
> p <- 2
> 
> y <- sapply(1:n, FUN=function(x){rnbinom(n=G, size=0.07, mu=200)})
> x <- sapply(1:p, FUN=function(x){rnorm(n=n, mean=n, sd=1)})
> 
> my_w <-  voom_weights(y, x, doPlot=TRUE)
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: voom_weights ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘TDAstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_barcode
> ### Title: Plot Persistent Homology as Topological Barcode
> ### Aliases: plot_barcode
> 
> ### ** Examples
> 
> 
> # create a 2-d point cloud of a circle (100 points)
> num.pts <- 100
> rand.angle <- runif(num.pts, 0, 2*pi)
> pt.cloud <- cbind(cos(rand.angle), sin(rand.angle))
> 
> # calculate persistent homology (num.pts by 3 numeric matrix)
> pers.hom <- calculate_homology(pt.cloud)
> 
> # plot calculated homology features as persistence diagram
> plot_barcode(pers.hom)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘inference.Rmd’ using rmarkdown
Quitting from lines 141-148 (inference.Rmd) 
Error: processing vignette 'inference.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘inference.Rmd’

--- re-building ‘inputformat.Rmd’ using rmarkdown
Quitting from lines 39-44 (inputformat.Rmd) 
Error: processing vignette 'inputformat.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘inputformat.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 171-173 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following files failed:
  ‘inference.Rmd’ ‘inputformat.Rmd’ ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tdr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TargetDiagram
> ### Title: Target Diagrams
> ### Aliases: targetDiagram target_diagram tdTheme
> 
> ### ** Examples
> 
> data(modelEx)
> 
> ## Compute statistics
> errModel <- applyStats(pvModels, pvObs)
> 
> ## Display results
> ## Default settings use type = 'quantile'
> targetDiagram(errModel, groups = model)
> 
> target_diagram(errModel, fill = 'model')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘TeachBayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bar_plot
> ### Title: Bar plot of numeric or character data
> ### Aliases: bar_plot
> 
> ### ** Examples
> 
>   s <- spinner_data(c(1, 2, 2, 1), nsim=100)
>   bar_plot(s, "Spinner Data")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘teamcolors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: teamcolors
> ### Title: Color palettes for professional sports teams
> ### Aliases: teamcolors
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(teamcolors)
> 
> if (require(Lahman) & require(dplyr)) {
+   pythag <- Teams %>%
+     filter(yearID == 2014) %>%
+     select(name, W, L, R, RA) %>%
+     mutate(wpct = W / (W+L), exp_wpct = 1 / (1 + (RA/R)^2)) %>%
+     # St. Louis Cardinals do not match
+     left_join(teamcolors, by = "name")
+   with(pythag, plot(exp_wpct, wpct, bg = primary, col = secondary, pch = 21, cex = 3))
+ 
+ 
+ # Using ggplot2
+ if (require(ggplot2)) {
+   ggplot(pythag, aes(x = wpct, y = exp_wpct, color = name, fill = name)) + 
+     geom_abline(slope = 1, intercept = 0, linetype = 3) + 
+     geom_point(shape = 21, size = 3) + 
+     scale_fill_manual(values = pythag$primary, guide = FALSE) + 
+     scale_color_manual(values = pythag$secondary, guide = FALSE) + 
+     geom_text(aes(label = substr(name, 1, 3))) + 
+     scale_x_continuous("Winning Percentage", limits = c(0.3, 0.7)) + 
+     scale_y_continuous("Expected Winning Percentage", limits = c(0.3, 0.7)) + 
+     coord_equal()
+   }
+ }
Loading required package: Lahman
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: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘telefit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eof
> ### Title: Performs an EOF decomposition of the data
> ### Aliases: eof
> 
> ### ** Examples
> 
> data("coprecip")
> attach(coprecip)
> 
> # compute ocean surface temperature eofs
> eofs = eof(Z)
> 
> # view first EOF, which corresponds to the El-Nino pattern
> coords.r.mod = coords.r
> coords.r.mod[,1][coords.r.mod[,1]>0] =
+   coords.r.mod[,1][coords.r.mod[,1]>0] - 360
> fields::quilt.plot(coords.r.mod, eofs$patterns[,1])
> 
> # alternatively, the plot.stData function can directly compute and plot EOFs
> plot(coprecip, type='eof', pattern=1)
Warning: Ignoring unknown aesthetics: z
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tensorBSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggtladleplot
> ### Title: Ladle plot for each mode of an object of class tladle using
> ###   ggplot2
> ### Aliases: ggtladleplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library(ICtest)
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: ggplot2
> n <- 500
> sig <- 0.6
> 
> Z <- rbind(sqrt(0.7)*rt(n,df=5)*sqrt(3/5),
+            sqrt(0.3)*runif(n,-sqrt(3),sqrt(3)),
+            sqrt(0.3)*(rchisq(n,df=3)-3)/sqrt(6),
+            sqrt(0.9)*(rexp(n)-1),
+            sqrt(0.1)*rlogis(n,0,sqrt(3)/pi),
+            sqrt(0.5)*(rbeta(n,2,2)-0.5)*sqrt(20)
+ )
> 
> dim(Z) <- c(3, 2, n)
> 
> U1 <- rorth(12)[,1:3]
> U2 <- rorth(8)[,1:2]
> U <- list(U1=U1, U2=U2)
> Y <- tensorTransform2(Z,U,1:2)
> EPS <- array(rnorm(12*8*n, mean=0, sd=sig), dim=c(12,8,n))
> X <- Y + EPS
> 
> 
> TEST <- tPCAladle(X, n.boot = 100)
> TEST
The tensorial Ladle based on tPCA gives for the data set X the dimension estimates:
Mode1 Mode2 
    1     2 
> ggtladleplot(TEST, crit = "gn")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GIAValidationExample.Rmd’ using rmarkdown
Quitting from lines 66-72 (GIAValidationExample.Rmd) 
Error: processing vignette 'GIAValidationExample.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GIAValidationExample.Rmd’

SUMMARY: processing the following file failed:
  ‘GIAValidationExample.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘testDriveR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kerrich
> ### Title: Kerrich Coin Toss Trial Outcomes
> ### Aliases: kerrich
> ### Keywords: datasets
> 
> ### ** Examples
> 
> str(kerrich)
'data.frame':	2000 obs. of  3 variables:
 $ id     : num  1 2 3 4 5 6 7 8 9 10 ...
 $ outcome: logi  FALSE FALSE FALSE TRUE TRUE TRUE ...
 $ average: num  0 0 0 0.25 0.4 ...
> 
> if (require("ggplot2")) {
+     ggplot(data = kerrich) +
+         geom_hline(mapping = aes(yintercept = .5, color = "p(heads)")) +
+         geom_line(mapping = aes(x = id, y = average)) +
+         ylim(0,1)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tetraclasse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gen_llosa
> ### Title: gen_llosa
> ### Aliases: gen_llosa
> 
> ### ** Examples
> 
> 
> 
> library(tetraclasse)
> gen_avis(100) %>%
+   prepare_base() %>%
+   gen_llosa()
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: %>% ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘texmex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chi
> ### Title: Measures of extremal dependence
> ### Aliases: chi summary.chi plot.chi print.chi ggplot.chi
> ###   print.summary.chi
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> 
> D <- liver[liver$dose == "D",]
> chiD <- chi(D[, 5:6])
> par(mfrow=c(1,2))
> ggplot(chiD)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Running examples in ‘texteffect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sibp_amce
> ### Title: Infer Treatments on the Test Set
> ### Aliases: sibp_amce sibp_amce_plot
> 
> ### ** Examples
> 
> ##Load the sample of Wikipedia biography data
> data(BioSample)
> 
> # Divide into training and test sets
> Y <- BioSample[,1]
> X <- BioSample[,-1]
> set.seed(1)
> train.ind <- sample(1:nrow(X), size = 0.5*nrow(X), replace = FALSE)
> 
> # Fit an sIBP on the training data
> sibp.fit <- sibp(X, Y, K = 2, alpha = 4, sigmasq.n = 0.8, 
+ 				 train.ind = train.ind)
[1] 10
[1] 14.17283
[1] 20
[1] 0.05200954
[1] 30
[1] 0.002362906
> 				 
> sibp.amce <- sibp_amce(sibp.fit, X, Y)
> sibp_amce_plot(sibp.amce)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘TextForecast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tv_sentiment_index
> ### Title: tv sentiment index function
> ### Aliases: tv_sentiment_index
> 
> ### ** Examples
> 
> suppressWarnings(RNGversion("3.5.0"))
> set.seed(1)
> data("stock_data")
> data("news_data")
> y=as.matrix(stock_data[,2])
> w=as.matrix(stock_data[,3])
> data("news_data")
> X=news_data[,2:ncol(news_data)]
> x=as.matrix(X)
> grid_alphas=0.05
> cont_folds=TRUE
> t=length(y)
> optimal_alphas=optimal_alphas(x[1:(t-1),],w[1:(t-1),],
+ y[2:t],grid_alphas,TRUE,"gaussian")
[1] 1
> tv_index <- tv_sentiment_index(x[1:(t-1),],w[1:(t-1),],y[2:t],
+ optimal_alphas[[1]],optimal_alphas[[2]],x,"gaussian",2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: tv_sentiment_index ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘thief-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AEdemand
> ### Title: Accident and Emergency demand in the UK
> ### Aliases: AEdemand
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> autoplot(AEdemand, xlab="Year", ylab="Demand ('000)") +
+   ggtitle("Accident & Emergency Demand in the UK")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tidybayes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare_levels
> ### Title: Compare the value of draws of some variable from a Bayesian
> ###   model for different levels of a factor
> ### Aliases: compare_levels
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(ggplot2)
> 
> data(RankCorr, package = "tidybayes")
> 
> # Let's do all pairwise comparisons of b[i,1]:
> RankCorr %>%
+   spread_draws(b[i,j]) %>%
+   filter(j == 1) %>%
+   compare_levels(b, by = i) %>%
+   median_qi()
# A tibble: 3 x 8
# Groups:   i [3]
  i         j     b   .lower .upper .width .point .interval
  <fct> <int> <dbl>    <dbl>  <dbl>  <dbl> <chr>  <chr>    
1 2 - 1     1 0.343 -0.00937  0.684   0.95 median qi       
2 3 - 1     1 0.734  0.416    1.08    0.95 median qi       
3 3 - 2     1 0.402 -0.0133   0.791   0.95 median qi       
> 
> # Or let's plot all comparisons against the first level (control):
> RankCorr %>%
+   spread_draws(b[i,j]) %>%
+   filter(j == 1) %>%
+   compare_levels(b, by = i, comparison = control) %>%
+   ggplot(aes(x = b, y = i)) +
+   geom_halfeyeh()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_tidyLPA.Rmd’ using rmarkdown
tidyLPA has received a major update, with a much easier workflow and improved functionality. However, you might have to update old syntax to account for the new workflow. See vignette('introduction-to-major-changes') for details!

Mplus is not installed. Use only package = 'mclust' when calling estimate_profiles().

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 115-121 (Introduction_to_tidyLPA.Rmd) 
Error: processing vignette 'Introduction_to_tidyLPA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction_to_tidyLPA.Rmd’

--- re-building ‘introduction-to-major-changes.Rmd’ using rmarkdown
--- finished re-building ‘introduction-to-major-changes.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction_to_tidyLPA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tidyquant-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coord_x_date
> ### Title: Zoom in on plot regions using date ranges or date-time ranges
> ### Aliases: coord_x_date coord_x_datetime
> 
> ### ** Examples
> 
> # Load libraries
> library(tidyquant)
> 
> # coord_x_date
> AAPL <- tq_get("AAPL")
> AAPL %>%
+     ggplot(aes(x = date, y = adjusted)) +
+     geom_line() +                         # Plot stock price
+     geom_ma(n = 50) +                 # Plot 50-day Moving Average
+     geom_ma(n = 200, color = "red") + # Plot 200-day Moving Average
+     coord_x_date(xlim = c(today() - weeks(12), today()),
+                ylim = c(100, 130))        # Zoom in
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘data-validation-rules.Rmd’ using rmarkdown
--- finished re-building ‘data-validation-rules.Rmd’

--- re-building ‘smells.Rmd’ using rmarkdown
Quitting from lines 141-157 (smells.Rmd) 
Error: processing vignette 'smells.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘smells.Rmd’

--- re-building ‘tidyxl.Rmd’ using rmarkdown
--- finished re-building ‘tidyxl.Rmd’

SUMMARY: processing the following file failed:
  ‘smells.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tigerstats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmGC
> ### Title: Linear Regression
> ### Aliases: lmGC
> 
> ### ** Examples
> 
> #To study the relationship between two numerical variables:
> lmGC(fastest~GPA,data=m111survey,graph=TRUE)

	Linear Regression

Correlation coefficient r =  -0.1406 

Equation of Regression Line:

	 fastest = 124.6956 + -5.8111 * GPA 

Residual Standard Error:	s   = 20.8833 
R^2 (unadjusted):		R^2 = 0.0198 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> -> print.GClm
Execution halted
Running examples in ‘tigger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotGenotype
> ### Title: Show a colorful representation of a genotype
> ### Aliases: plotGenotype
> 
> ### ** Examples
> 
> # Plot genotype
> plotGenotype(SampleGenotype)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotGenotype ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
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

Quitting from lines 146-148 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘timeline-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: timeline
> ### Title: Creates a timeline plot.
> ### Aliases: timeline
> 
> ### ** Examples
> 
> data(ww2)
> timeline(ww2, ww2.events)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot_timeline.Rmd’ using knitr
Quitting from lines 51-53 (plot_timeline.Rmd) 
Error: processing vignette 'plot_timeline.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'plot_timeline.Rmd'

SUMMARY: processing the following file failed:
  'plot_timeline.Rmd'

Error: Vignette re-building failed.
Execution halted
Running examples in ‘timelineS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: durPlot
> ### Title: Graphs and Summary for Date Durations
> ### Aliases: durPlot
> 
> ### ** Examples
> 
> durPlot(life_exp, start = "Birth", end = "Death", group = "Country",
+ timeunit = "years", facet = TRUE, binwidth = 3, alpha = 0.7, title = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: durPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘TimeProjection-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalendarHeatmap
> ### Title: Calendar Heatmap
> ### Aliases: plotCalendarHeatmap
> 
> ### ** Examples
> 
> dates = timeSequence(from = '2012-01-01', to = '2012-12-31', by = 'day')
>    plotCalendarHeatmap(as.Date(dates), 1:366)
Loading required package: ggplot2
Loading required package: plyr

Attaching package: ‘plyr’

The following object is masked from ‘package:lubridate’:

    here

Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tintHTML.Rmd’ using rmarkdown
Quitting from lines 28-30 (tintHTML.Rmd) 
Error: processing vignette 'tintHTML.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tintHTML.Rmd’

--- re-building ‘tintPDF.Rmd’ using rmarkdown
Quitting from lines 28-30 (tintPDF.Rmd) 
Error: processing vignette 'tintPDF.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tintPDF.Rmd’

SUMMARY: processing the following files failed:
  ‘tintHTML.Rmd’ ‘tintPDF.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘TippingPoint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TippingPoint
> ### Title: Generic function for Enhanced Tipping Point Displays
> ### Aliases: TippingPoint
> 
> ### ** Examples
> 
> TippingPoint(outcome=tippingdata$binary, treat= tippingdata$treat,
+   group.infor=TRUE, plot.type = "estimate",ind.values = TRUE,
+   impValuesT  = NA,  impValuesC = NA,
+   summary.type = "density", alpha = 0.95, S=1.5, n.grid = 100,
+   HistMeanT = c(0.38,0.4), HistMeanC =  c(0.2,0.55))

Group Information:

Groups                    	Treatment 	Control
Size                     	 150      	 120      
Number of nonrespondents 	 13       	 27       
% of nonrespondents      	 0.08666667 	 0.225    
Observed proportion      	 0.5328467 	 0.5376344 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TippingPoint.Rmd’ using rmarkdown
Quitting from lines 53-100 (TippingPoint.Rmd) 
Error: processing vignette 'TippingPoint.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TippingPoint.Rmd’

SUMMARY: processing the following file failed:
  ‘TippingPoint.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fortify.tis
> ### Title: Fortify a tis object
> ### Aliases: fortify.tis
> 
> ### ** Examples
> 
>     if(require("ggplot2") && require("reshape")) {
+              # Examples of plotting tis series with ggplot2
+              require("datasets")
+              require("scales")
+ 
+              # univariate example
+              num_discoveries <- as.tis(discoveries)
+              ggplot(data = fortify(num_discoveries, offset=0)) + 
+                     geom_line(aes(x=date, y=num_discoveries)) + 
+                     scale_x_date(breaks = date_breaks("10 years"), labels = date_format("%Y"))
+              
+              # multivariate example using the "melt trick"
+              Seatbelts.tis <- as.tis(Seatbelts[ , c("drivers", "front", "rear")])
+              Seatbelt.names <- c("Driver", "Front Seat Passenger", "Back Seat Passenger")
+              Seatbelts.df <- fortify(Seatbelts.tis, dfNames = Seatbelt.names,
+                                      timeName = "Time")
+              Seatbelts.dfm <- melt(Seatbelts.df, id.var = "Time", variable_name="type")
+              qplot( Time, value, data = Seatbelts.dfm, geom="line", 
+                     group=type, colour=type, linetype=type ) + 
+                  geom_vline(xintercept=as.numeric(as.Date("1983-01-31")), 
+                     colour="black", linetype="dashed") +
+                  ylab("Monthly Road Casulties in the UK")
+     }
Loading required package: ggplot2
Loading required package: reshape
Loading required package: scales
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_of_computation_time.Rmd’ using rmarkdown
Loading required package: Rcpp

Attaching package: 'lmom'

The following objects are masked from 'package:lmomco':

    cdfexp, cdfgam, cdfgev, cdfglo, cdfgno, cdfgpa, cdfgum,
    cdfkap, cdfln3, cdfnor, cdfpe3, cdfwak, cdfwei, quaexp,
    quagam, quagev, quaglo, quagno, quagpa, quagum, quakap,
    qualn3, quanor, quape3, quawak, quawei

--- finished re-building ‘comparison_of_computation_time.Rmd’

--- re-building ‘short_introduction.Rmd’ using rmarkdown
Quitting from lines 100-103 (short_introduction.Rmd) 
Error: processing vignette 'short_introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘short_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘short_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_symbols
> ### Title: Draw symbols
> ### Aliases: tm_symbols tm_squares tm_bubbles tm_dots tm_markers
> ### Keywords: map symbol
> 
> ### ** Examples
> 
> data(World, metro)
> metro$growth <- (metro$pop2020 - metro$pop2010) / (metro$pop2010 * 10) * 100
> 
> tm_shape(World) +
+     tm_fill("grey70") +
+ tm_shape(metro) +
+     tm_bubbles("pop2010", col = "growth", 
+         border.col = "black", border.alpha = .5, 
+         style="fixed", breaks=c(-Inf, seq(0, 6, by=2), Inf),
+         palette="-RdYlBu", contrast=1, 
+         title.size="Metro population", 
+         title.col="Growth rate (%)") + 
+ tm_format("World")
Variable "growth" contains positive and negative values, so midpoint is set to 0. Set midpoint = NA to show the full spectrum of the color palette.
> 
> tm_shape(metro) +
+ 	tm_symbols(size = "pop2010", col="pop2010", shape="pop2010",
+ 		legend.format = list(text.align="right", text.to.columns = TRUE)) +
+ tm_legend(outside = TRUE, outside.position = "bottom", stack = "horizontal")
Error in unit(as.numeric(unt) * b + a, cls) : Invalid unit
Calls: <Anonymous> ... FUN -> do.call -> lapply -> FUN -> unit_mod -> unit
Execution halted
Running examples in ‘Tmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_na
> ### Title: Plot missing data
> ### Aliases: gg_na
> ### Keywords: NA
> 
> ### ** Examples
> 
> # What a mess. 
> # Feature 10 is missing a lot. Observations 25 and 35 are completely missing.
> # Most of features 40-45 are missing, except for the first few observations.
> set.seed(2016-07-12)
> x <- matrix(1, nrow=50, ncol=50)
> x[sample(prod(dim(x)), 100)] <- NA
> x <- data.frame(x)
> x$X10[sample(length(x$X10), 25)] <- NA
> x[c(25, 35), ] <- NA
> x[1:40, 40:45] <- NA
> gg_na(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tourr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: path_curves
> ### Title: Draw the path that the geodesics took.
> ### Aliases: path_curves
> 
> ### ** Examples
> 
> path1d <- save_history(flea[, 1:6], grand_tour(1), 10)
> path2d <- save_history(flea[, 1:6], grand_tour(2), 10)
> 
> if (require("ggplot2")) {
+ plot(path_curves(path1d))
+ plot(path_curves(interpolate(path1d)))
+ 
+ plot(path_curves(path2d))
+ plot(path_curves(interpolate(path2d)))
+ 
+ # Instead of relying on the built in plot method, you might want to
+ # generate your own.  Here are few examples of alternative displays:
+ 
+ df <- path_curves(path2d)
+ qplot(step, value, data = df, group = obs:var, geom = "line", colour=var) + facet_wrap( ~ obs)
+ 
+ library(reshape2)
+ qplot(`1`, `2`, data = dcast(df, ... ~ var)) +
+   facet_wrap( ~ step) +
+   coord_equal()
+ }
Loading required package: ggplot2
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘toxEval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_chem_data
> ### Title: Grouped Boxplots
> ### Aliases: graph_chem_data plot_tox_boxplots tox_boxplot_data
> 
> ### ** Examples
> 
> # This is the example workflow:
> path_to_tox <-  system.file("extdata", package="toxEval")
> file_name <- "OWC_data_fromSup.xlsx"
> 
> full_path <- file.path(path_to_tox, file_name)
> 
> tox_list <- create_toxEval(full_path)
> ACC <- get_ACC(tox_list$chem_info$CAS)
> ACC <- remove_flags(ACC)
> 
> cleaned_ep <- clean_endPoint_info(end_point_info)
> filtered_ep <- filter_groups(cleaned_ep)
> chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
> plot_tox_boxplots(chemical_summary, "Biological")   
Warning: Removed 1 rows containing missing values (geom_hline).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘PrepareData.Rmd’ using rmarkdown
--- finished re-building ‘PrepareData.Rmd’

--- re-building ‘basicWorkflow.Rmd’ using rmarkdown
USGS Research Package:
https://owi.usgs.gov/R/packages.html#research
Warning: Removed 1 rows containing missing values (geom_hline).
Quitting from lines 179-184 (basicWorkflow.Rmd) 
Error: processing vignette 'basicWorkflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘basicWorkflow.Rmd’

--- re-building ‘benchmarks.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

USGS Research Package:
https://owi.usgs.gov/R/packages.html#research
Warning: Removed 1 rows containing missing values (geom_hline).
Quitting from lines 192-202 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘benchmarks.Rmd’

--- re-building ‘shinyApp.Rmd’ using rmarkdown
--- finished re-building ‘shinyApp.Rmd’

SUMMARY: processing the following files failed:
  ‘basicWorkflow.Rmd’ ‘benchmarks.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TPD.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: ks
Quitting from lines 106-107 (TPD.Rmd) 
Error: processing vignette 'TPD.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TPD.Rmd’

SUMMARY: processing the following file failed:
  ‘TPD.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘TPMplt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TPM2dplt
> ### Title: Plot 2d thermal process maps
> ### Aliases: TPM2dplt
> ### Keywords: PLTbuilder Processing-map
> 
> ### ** Examples
> 
> epstable <- epsExtract(TPMdata, 0.7, 2, 3)
> DMM <- DMMprocess(epstable)
> PLTbd <- SVRModel(DMM)
> TPM2dplt(PLTbd)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TPMplt-vignette.Rmd’ using rmarkdown
Quitting from lines 166-167 (TPMplt-vignette.Rmd) 
Error: processing vignette 'TPMplt-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TPMplt-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘TPMplt-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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-patched-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Quitting from lines 75-80 (demo.Rmd) 
Error: processing vignette 'demo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘demo.Rmd’

--- re-building ‘demo_estimate_effective_sample_size.Rmd’ using rmarkdown
Quitting from lines 54-65 (demo_estimate_effective_sample_size.Rmd) 
Error: processing vignette 'demo_estimate_effective_sample_size.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘demo_estimate_effective_sample_size.Rmd’

--- re-building ‘profile_calc_act.Rmd’ using rmarkdown
Quitting from lines 63-69 (profile_calc_act.Rmd) 
Error: processing vignette 'profile_calc_act.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘profile_calc_act.Rmd’

--- re-building ‘profile_calc_esses.Rmd’ using rmarkdown
--- finished re-building ‘profile_calc_esses.Rmd’

--- re-building ‘read_beast2_trees.Rmd’ using rmarkdown
--- finished re-building ‘read_beast2_trees.Rmd’

SUMMARY: processing the following files failed:
  ‘demo.Rmd’ ‘demo_estimate_effective_sample_size.Rmd’
  ‘profile_calc_act.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘trackeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: zones
> ### Title: Time spent in training zones.
> ### Aliases: zones
> 
> ### ** Examples
> 
> data('run', package = 'trackeR')
> runZones <- zones(run, what = 'speed', breaks = list(speed = c(0, 2:6, 12.5)))
> ## if breaks is a named list, argument 'what' can be left unspecified
> runZones <- zones(run, breaks = list(speed = c(0, 2:6, 12.5)))
> ## if only a single variable is to be evaluated, 'breaks' can also be a vector
> runZones <- zones(run, what = 'speed', breaks = c(0, 2:6, 12.5))
> plot(runZones)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
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

Quitting from lines 86-87 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

The following object is masked from 'package:base':

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Error: processing vignette 'trackeR.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'trackeR.Rnw'

SUMMARY: processing the following files failed:
  ‘TourDetrackeR.Rmd’ ‘trackeR.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
Loading required package: histry
--- finished re-building ‘index.Rmd’

--- re-building ‘Extending-trackr.Rnw’ using knitr
Quitting from lines 146-155 (Extending-trackr.Rnw) 
Error: processing vignette 'Extending-trackr.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Extending-trackr.Rnw’

SUMMARY: processing the following file failed:
  ‘Extending-trackr.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TrajDataMining.Rmd’ using rmarkdown
Quitting from lines 49-54 (TrajDataMining.Rmd) 
Error: processing vignette 'TrajDataMining.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TrajDataMining.Rmd’

SUMMARY: processing the following file failed:
  ‘TrajDataMining.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘trapezoid.Rnw’ using Sweave
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2

Error: processing vignette 'trapezoid.Rnw' failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘trapezoid.Rnw’

SUMMARY: processing the following file failed:
  ‘trapezoid.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tree.bins.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'data.table'

The following objects are masked from 'package:dplyr':

    between, first, last

Quitting from lines 40-52 (tree.bins.Rmd) 
Error: processing vignette 'tree.bins.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tree.bins.Rmd’

SUMMARY: processing the following file failed:
  ‘tree.bins.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘treecm.Rnw’ using Sweave
Error: processing vignette 'treecm.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘treecm.Rnw’

SUMMARY: processing the following file failed:
  ‘treecm.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘treeDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.treedacv
> ### Title: Plot a treedacv object
> ### Aliases: plot.treedacv
> 
> ### ** Examples
> 
> data(treeda_example)
> out.treedacv = treedacv(response = treeda_example$response,
+     predictors = treeda_example$predictors,
+     tree = treeda_example$tree,
+     pvec = 1:10)
> plot(out.treedacv)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘treeda-vignette.Rmd’ using rmarkdown
Quitting from lines 181-183 (treeda-vignette.Rmd) 
Error: processing vignette 'treeda-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘treeda-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘treeda-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘h3n2.Rmd’ using rmarkdown
Quitting from lines 182-184 (h3n2.Rmd) 
Error: processing vignette 'h3n2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘h3n2.Rmd’

SUMMARY: processing the following file failed:
  ‘h3n2.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘TreeDep-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TreeDep_plot
> ### Title: TreeDep_plot - Generates a plot for selected variables and
> ###   dates.
> ### Aliases: TreeDep_plot
> 
> ### ** Examples
> 
> 
> TreeDep_plot(my_data = Bizkaia_data,
+ variable1 = "Dep_PM10",
+ variable2 = "Wind",
+ start_month = 6,
+ stop_month = 7,
+ start_day = 25,
+ stop_day = 3)
Warning: Removed 12 rows containing missing values (geom_path).
Warning: Removed 12 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘treemapify-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_treemap
> ### Title: A 'ggplot2' geom to draw a treemap.
> ### Aliases: geom_treemap
> 
> ### ** Examples
> 
> 
> ggplot2::ggplot(G20, ggplot2::aes(area = gdp_mil_usd, fill = region)) +
+  geom_treemap()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-treemapify.Rmd’ using rmarkdown
Quitting from lines 35-37 (introduction-to-treemapify.Rmd) 
Error: processing vignette 'introduction-to-treemapify.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-treemapify.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-treemapify.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘treespace-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: treespace
> ### Title: Phylogenetic tree exploration
> ### Aliases: treespace
> 
> ### ** Examples
> 
> 
> ## generate list of trees
> x <- rmtree(10, 20)
> names(x) <- paste("tree", 1:10, sep = "")
> 
> ## use treespace
> res <- treespace(x, nf=3)
> table.paint(as.matrix(res$D))
> scatter(res$pco)
> 
> data(woodmiceTrees)
> woodmiceDists <- treespace(woodmiceTrees,nf=3)
> plot(woodmiceDists$pco$li[,1],woodmiceDists$pco$li[,2])
> woodmicedf <- woodmiceDists$pco$li
> if(require(ggplot2)){
+ woodmiceplot <- ggplot(woodmicedf, aes(x=A1, y=A2)) # create plot
+ woodmiceplot + geom_density2d(colour="gray80") + # contour lines
+ geom_point(size=6, shape=1, colour="gray50") + # grey edges
+ geom_point(size=6, alpha=0.2, colour="navy") + # transparent blue points
+ xlab("") + ylab("") + theme_bw(base_family="") # remove axis labels and grey background
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [13s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  Registered S3 method overwritten by 'trelliscopejs':
    method from   
    +.gg   ggplot2
  > 
  > test_check("trelliscopejs")
  ── 1. Error: examples run without barfing (@test-trelliscope.R#51)  ────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: mpg %>% group_by(manufacturer, class) %>% nest() %>% mutate(panel = map_plot(data, 
         ~qplot(cty, hwy, data = .) + xlab("cty") + ylab("hwy") + xlim(7, 37) + ylim(9, 
             47) + theme_bw())) %>% trelliscope(name = "tidy_gg", thumb = FALSE) at testthat/test-trelliscope.R:51
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: withVisible(function_list[[k]](value))
  8: function_list[[k]](value)
  9: trelliscope(., name = "tidy_gg", thumb = FALSE)
  10: trelliscope.data.frame(., name = "tidy_gg", thumb = FALSE)
  ...
  25: preDraw(x)
  26: preDraw.gTree(x)
  27: pushvpgp(x)
  28: pushgrobvp(x$vp)
  29: pushgrobvp.viewport(x$vp)
  30: pushViewport(vp, recording = FALSE)
  31: lapply(vps, push.vp, recording)
  32: FUN(X[[i]], ...)
  33: push.vp.viewport(X[[i]], ...)
  34: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 224 SKIPPED: 0 FAILED: 1
  1. Error: examples run without barfing (@test-trelliscope.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘tricolore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorKeySextant
> ### Title: Sextant Scheme Legend
> ### Aliases: ColorKeySextant
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKeySextant(center = prop.table(runif(3)),
+                            values = c('#01A0C6', '#B8B3D8', '#F11D8C',
+                                       '#FFB3B3', '#FFFF00', '#B3DCC3'),
+                            label_as = 'pct_diff', show_center = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Quitting from lines 64-75 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘trinROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: roc.eda
> ### Title: Exploratory data analysis for a three-class ROC marker
> ### Aliases: roc.eda
> 
> ### ** Examples
> 
> data(krebs)
> 
> # empirical EDA:
> roc.eda(dat = krebs[,c(1,5)], type = "e", plotVUS = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: roc.eda ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (require("testthat", character.only = TRUE)) {
  +   test_check("trinROC")
  + }
  Loading required package: testthat
  Loading required package: trinROC
  ── 1. Failure: boot.test() function (@test_trinROC.R#50)  ──────────────────────
  round(temp$p.value, 2) not equal to 0.24.
  1/1 mismatches
  [1] 0.25 - 0.24 == 0.01
  
  ── 2. Failure: boot.test() function (@test_trinROC.R#56)  ──────────────────────
  unname(round(temp$statistic, 3)) not equal to 0.537.
  1/1 mismatches
  [1] 0.534 - 0.537 == -0.003
  
  ── 3. Error: roc.eda(), whole functionality (@test_trinROC.R#115)  ─────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: roc.eda(dat = dat[, 1:2], plotVUS = FALSE) at testthat/test_trinROC.R:115
  2: grid.arrange(histROC, meas.overview, ncol = 2)
  3: grid.draw(g)
  4: grid.draw.gTree(g)
  5: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  6: drawGTree(x)
  7: grid.draw(x$children[[i]], recording = FALSE)
  8: grid.draw.gTree(x$children[[i]], recording = FALSE)
  9: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  10: drawGTree(x)
  ...
  14: pushgrobvp(x$vp)
  15: pushgrobvp.viewport(x$vp)
  16: pushViewport(vp, recording = FALSE)
  17: lapply(vps, push.vp, recording)
  18: FUN(X[[i]], ...)
  19: push.vp.vpStack(X[[i]], ...)
  20: lapply(vp, push.vp, recording)
  21: FUN(X[[i]], ...)
  22: push.vp.viewport(X[[i]], ...)
  23: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 35 SKIPPED: 0 FAILED: 3
  1. Failure: boot.test() function (@test_trinROC.R#50) 
  2. Failure: boot.test() function (@test_trinROC.R#56) 
  3. Error: roc.eda(), whole functionality (@test_trinROC.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘trinROC_vignette.Rmd’ using rmarkdown
Quitting from lines 190-229 (trinROC_vignette.Rmd) 
Error: processing vignette 'trinROC_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘trinROC_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘trinROC_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘TripleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_missings
> ### Title: Plot missing values
> ### Aliases: plot_missings
> 
> ### ** Examples
> 
> data(multiGroup)
> m2 <- multiGroup
> m2$ex[m2$perceiver.id==90201] <- NA
> m2$ex[m2$perceiver.id>92001] <- NA
> m2$ex[sample(nrow(m2),  1000)] <- NA
> plot_missings(ex~perceiver.id*target.id|group.id, data=m2)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘tsBSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AMUSEladle
> ### Title: Ladle Estimator to Estimate the Number of White Noise Components
> ###   in SOS with AMUSE
> ### Aliases: AMUSEladle
> ### Keywords: multivariate ts
> 
> ### ** Examples
> 
>   n <- 1000
>   
>   s1 <- arima.sim(n = n, list(ar = 0.6, ma = c(0, -0.4)))
>   s2 <- arima.sim(n = n, list(ar = c(0.4,0.1,0.3), ma = c(0.2, 0.4)))
>   s3 <- arima.sim(n = n, list(ar = c(0.7, 0.1)))
>   Snoise <- matrix(rnorm(5*n), ncol = 5)
>   S <- cbind(s1, s2, s3, Snoise)
> 
>   A <- matrix(rnorm(64), 8, 8)
>   X <- S %*% t(A)
>   
>   ladle_AMUSE <- AMUSEladle(X, l = 20, sim = "geom")
> 
>   # The estimated number on non-white-noise components
>   summary(ladle_AMUSE)

AMUSE Ladle estimator for X 
k:  3
>   
>   # The ladle plot
>   ladleplot(ladle_AMUSE)
>   # Using ggplot
>   ggladleplot(ladle_AMUSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsfeatures.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

trying URL ‘https://github.com/robjhyndman/tsfeatures/raw/master/extra-data/yahoo.rda’
Content type 'application/octet-stream' length 7897660 bytes (7.5 MB)
==================================================
downloaded 7.5 MB

trying URL ‘https://github.com/robjhyndman/tsfeatures/raw/master/extra-data/hwl.rda’
Content type 'application/octet-stream' length 185319 bytes (180 KB)
==================================================
downloaded 180 KB

Quitting from lines 412-421 (tsfeatures.Rmd) 
Error: processing vignette 'tsfeatures.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tsfeatures.Rmd’

SUMMARY: processing the following file failed:
  ‘tsfeatures.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tsfknn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.knnForecast
> ### Title: Create a ggplot object from a knnForecast object
> ### Aliases: autoplot.knnForecast
> 
> ### ** Examples
> 
> pred <- knn_forecasting(USAccDeaths, h = 12, lags = 1:12, k = 2)
> library(ggplot2)
> autoplot(pred)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsfknn.Rmd’ using rmarkdown
geom_path: Each group consists of only one observation. Do you need to
adjust the group aesthetic?
geom_path: Each group consists of only one observation. Do you need to
adjust the group aesthetic?
Quitting from lines 120-122 (tsfknn.Rmd) 
Error: processing vignette 'tsfknn.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tsfknn.Rmd’

SUMMARY: processing the following file failed:
  ‘tsfknn.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tsibble-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: count_gaps
> ### Title: Count implicit gaps
> ### Aliases: count_gaps
> 
> ### ** Examples
> 
> ped_gaps <- pedestrian %>% 
+   count_gaps(.full = TRUE)
> if (!requireNamespace("ggplot2", quietly = TRUE)) {
+   stop("Please install the ggplot2 package to run these following examples.")
+ }
> library(ggplot2)
> ggplot(ped_gaps, aes(x = Sensor, colour = Sensor)) +
+   geom_linerange(aes(ymin = .from, ymax = .to)) +
+   geom_point(aes(y = .from)) +
+   geom_point(aes(y = .to)) +
+   coord_flip() +
+   theme(legend.position = "bottom")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘faq.Rmd’ using rmarkdown

Attaching package: 'tsibble'

The following object is masked from 'package:stats':

    filter


Attaching package: 'lubridate'

The following objects are masked from 'package:tsibble':

    interval, new_interval

The following object is masked from 'package:base':

    date

--- finished re-building ‘faq.Rmd’

--- re-building ‘implicit-na.Rmd’ using rmarkdown

Attaching package: 'tsibble'

The following object is masked from 'package:stats':

    filter

Quitting from lines 44-51 (implicit-na.Rmd) 
Error: processing vignette 'implicit-na.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘implicit-na.Rmd’

--- re-building ‘intro-tsibble.Rmd’ using rmarkdown

Attaching package: 'tsibble'

The following object is masked from 'package:stats':

    filter


Attaching package: 'lubridate'

The following objects are masked from 'package:tsibble':

    interval, new_interval

The following object is masked from 'package:base':

    date

--- finished re-building ‘intro-tsibble.Rmd’

--- re-building ‘window.Rmd’ using rmarkdown

Attaching package: 'tsibble'

The following object is masked from 'package:stats':

    filter


Attaching package: 'dplyr'

The following object is masked from 'package:tsibble':

    id

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘window.Rmd’

SUMMARY: processing the following file failed:
  ‘implicit-na.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘tsiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: maxthreshold
> ### Title: maxthreshold
> ### Aliases: maxthreshold
> 
> ### ** Examples
> 
> require(kernlab)
Loading required package: kernlab
> Mold <- twentymeas[["Mold"]]
> plotdata(Mold)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘TSMining-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BuildOperation
> ### Title: An example 1-week data set containing the power consumption data
> ###   of two building services sub-systems
> ### Aliases: BuildOperation
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> data(BuildOperation)
> ggplot(data = BuildOperation, aes(x = 1:dim(BuildOperation)[1], y = WCC)) +
+  geom_line() + geom_point()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘tspmeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: morph_instances
> ### Title: Morphing (convex-combination) of two instances with parameter
> ###   alpha.
> ### Aliases: morph_instances
> 
> ### ** Examples
> 
> x = random_instance(10)
> y = random_instance(10)
> z = morph_instances(x, y, 0.5)
> autoplot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘TSrepr_extentions.Rmd’ using rmarkdown
Quitting from lines 26-38 (TSrepr_extentions.Rmd) 
Error: processing vignette 'TSrepr_extentions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TSrepr_extentions.Rmd’

--- re-building ‘TSrepr_representations_of_time_series.Rmd’ using rmarkdown
Quitting from lines 89-96 (TSrepr_representations_of_time_series.Rmd) 
Error: processing vignette 'TSrepr_representations_of_time_series.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TSrepr_representations_of_time_series.Rmd’

--- re-building ‘TSrepr_representations_use_case.Rmd’ using rmarkdown
Warning in melt.data.table(data.table(class = as.factor(res_km$cluster),  :
  To be consistent with reshape2's melt, id.vars and measure.vars are internally guessed when both are 'NULL'. All non-numeric/integer/logical type columns are considered id.vars, which in this case are columns [class]. Consider providing at least one of 'id' or 'measure' vars in future.
Quitting from lines 51-68 (TSrepr_representations_use_case.Rmd) 
Error: processing vignette 'TSrepr_representations_use_case.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TSrepr_representations_use_case.Rmd’

SUMMARY: processing the following files failed:
  ‘TSrepr_extentions.Rmd’ ‘TSrepr_representations_of_time_series.Rmd’
  ‘TSrepr_representations_use_case.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Running examples in ‘tvm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rate_curve
> ### Title: Plots a rate curve
> ### Aliases: plot.rate_curve
> 
> ### ** Examples
> 
> r <- rate_curve(rates = c(0.1, 0.2, 0.3), rate_type = "zero_eff")
> plot(r)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 72-75 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘UBL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbC
> ### Title: Synthetic Imbalanced Data Set for a Multi-class Task
> ### Aliases: ImbC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2

Attaching package: ‘ggplot2’

The following object is masked from ‘package:randomForest’:

    margin

> data(ImbC)
> summary(ImbC)
       X1              X2         Class    
 Min.   :-13.5843   cat :300   normal:859  
 1st Qu.: -2.6930   dog :400   rare1 : 10  
 Median : -0.1592   fish:300   rare2 :131  
 Mean   : -0.1064                          
 3rd Qu.:  2.4633                          
 Max.   : 12.7836                          
> ggplot(data=ImbC, aes(x=X2, y=X1, color=Class))+geom_jitter()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ufs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: associationsDiamondPlot
> ### Title: A diamondplot with confidence intervals for associations
> ### Aliases: associationsDiamondPlot associationsToDiamondPlotDf
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> ### Simple diamond plot with correlations
> ### and their confidence intervals
> 
> associationsDiamondPlot(mtcars,
+                         covariates=c('cyl', 'hp', 'drat', 'wt',
+                                      'am', 'gear', 'vs', 'carb', 'qsec'),
+                         criteria='mpg');
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Umatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMatrix
> ### Title: plotMatrix
> ### Aliases: plotMatrix
> 
> ### ** Examples
> 
> data("Hepta")
> e = esomTrain(Hepta$Data, Key = 1:nrow(Hepta$Data))
[1] "Epoch: 1 started"
[1] "Epoch: 2 started"
[1] "Epoch: 3 started"
[1] "Epoch: 4 started"
[1] "Epoch: 5 started"
[1] "Epoch: 6 started"
[1] "Epoch: 7 started"
[1] "Epoch: 8 started"
[1] "Epoch: 9 started"
[1] "Epoch: 10 started"
[1] "Epoch: 11 started"
[1] "Epoch: 12 started"
[1] "Epoch: 13 started"
[1] "Epoch: 14 started"
[1] "Epoch: 15 started"
[1] "Epoch: 16 started"
[1] "Epoch: 17 started"
[1] "Epoch: 18 started"
[1] "Epoch: 19 started"
[1] "Epoch: 20 started"
[1] "Epoch: 21 started"
[1] "Epoch: 22 started"
[1] "Epoch: 23 started"
[1] "Epoch: 24 started"
[1] "---- Esom Training Finished ----"
[1] "shift to point of highest density"
> plotMatrix(e$Umatrix,e$BestMatches)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tmx_genotypic_effect
> ### Title: Graphical display of genotypic effects.
> ### Aliases: tmx_genotypic_effect
> 
> ### ** Examples
> 
> library(umx);
> tmx_genotypic_effect(p = .5, q =.5, a =.5, d = 1, m = 0)
Genotype frequencies at Hardy Weinberg Equilibrium (p= 0.5 q = 0.5)


|Genotypes |BB   |Bb  |bb   |
|:---------|:----|:---|:----|
|Frequency |p²   |2pq |q²   |
|fraction  |0.25 |0.5 |0.25 |
Warning: Using size for a discrete variable is not advised.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: tmx_genotypic_effect ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘test_unifDAG.R’ [5s/5s]
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘measurement_units_in_R.Rmd’ using rmarkdown
Quitting from lines 360-363 (measurement_units_in_R.Rmd) 
Error: processing vignette 'measurement_units_in_R.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘measurement_units_in_R.Rmd’

--- re-building ‘units.Rmd’ using rmarkdown
--- finished re-building ‘units.Rmd’

SUMMARY: processing the following file failed:
  ‘measurement_units_in_R.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘unvotes.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning: code chunks must not depend on the uncached chunk "joined"
Warning: Column `rcid` has different attributes on LHS and RHS of join
Warning: code chunks must not depend on the uncached chunk "by_country_year"

Attaching package: 'lubridate'

The following object is masked from 'package:base':

    date

Quitting from lines 76-87 (unvotes.Rmd) 
Error: processing vignette 'unvotes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘unvotes.Rmd’

SUMMARY: processing the following file failed:
  ‘unvotes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘updog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flexdog
> ### Title: Flexible genotyping for polyploids from next-generation
> ###   sequencing data.
> ### Aliases: flexdog
> 
> ### ** Examples
> 
> 
> ## A natural population. We will assume a
> ## normal prior since there are so few
> ## individuals.
> data("uitdewilligen")
> ploidy  <- 4
> refvec  <- uitdewilligen$refmat[, 1]
> sizevec <- uitdewilligen$sizemat[, 1]
> fout    <- flexdog(refvec  = refvec,
+                    sizevec = sizevec,
+                    ploidy  = ploidy,
+                    model   = "norm")
         Fit: 1 of 5 
Initial Bias: 0.3678794 
Log-Likelihood: -20.89589 
Keeping new fit.

         Fit: 2 of 5 
Initial Bias: 0.6065307 
Log-Likelihood: -20.19809 
Keeping new fit.

         Fit: 3 of 5 
Initial Bias: 1 
Log-Likelihood: -20.67759 
Keeping old fit.

         Fit: 4 of 5 
Initial Bias: 1.648721 
Log-Likelihood: -20.67754 
Keeping old fit.

         Fit: 5 of 5 
Initial Bias: 2.718282 
Log-Likelihood: -20.67754 
Keeping old fit.

Done!
> plot(fout)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘UpSetR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: upset
> ### Title: UpSetR Plot
> ### Aliases: upset
> 
> ### ** Examples
> 
> movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), header=TRUE, sep=";" )
> 
> require(ggplot2); require(plyr); require(gridExtra); require(grid);
Loading required package: ggplot2
Loading required package: plyr
Loading required package: gridExtra
Loading required package: grid
> 
> between <- function(row, min, max){
+   newData <- (row["ReleaseDate"] < max) & (row["ReleaseDate"] > min)
+ }
> 
> plot1 <- function(mydata, x){
+   myplot <- (ggplot(mydata, aes_string(x= x, fill = "color"))
+             + geom_histogram() + scale_fill_identity()
+             + theme(plot.margin = unit(c(0,0,0,0), "cm")))
+ }
> 
> plot2 <- function(mydata, x, y){
+   myplot <- (ggplot(data = mydata, aes_string(x=x, y=y, colour = "color"), alpha = 0.5)
+             + geom_point() + scale_color_identity()
+             + theme_bw() + theme(plot.margin = unit(c(0,0,0,0), "cm")))
+ }
> 
> attributeplots <- list(gridrows = 55,
+                   plots = list(list(plot = plot1, x= "ReleaseDate",  queries = FALSE),
+                          list(plot = plot1, x= "ReleaseDate", queries = TRUE),
+                          list(plot = plot2, x = "ReleaseDate", y = "AvgRating", queries = FALSE),
+                          list(plot = plot2, x = "ReleaseDate", y = "AvgRating", queries = TRUE)),
+                    ncols = 3)
> 
> upset(movies, nsets = 7, nintersects = 30, mb.ratio = c(0.5, 0.5),
+       order.by = c("freq", "degree"), decreasing = c(TRUE,FALSE))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: upset ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘attribute.plots.Rmd’ using rmarkdown
Quitting from lines 46-47 (attribute.plots.Rmd) 
Error: processing vignette 'attribute.plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘attribute.plots.Rmd’

--- re-building ‘basic.usage.Rmd’ using rmarkdown
Quitting from lines 32-33 (basic.usage.Rmd) 
Error: processing vignette 'basic.usage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘basic.usage.Rmd’

--- re-building ‘queries.Rmd’ using rmarkdown
Quitting from lines 40-41 (queries.Rmd) 
Error: processing vignette 'queries.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘queries.Rmd’

--- re-building ‘set.metadata.plots.Rmd’ using rmarkdown
Quitting from lines 63-64 (set.metadata.plots.Rmd) 
Error: processing vignette 'set.metadata.plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘set.metadata.plots.Rmd’

SUMMARY: processing the following files failed:
  ‘attribute.plots.Rmd’ ‘basic.usage.Rmd’ ‘queries.Rmd’
  ‘set.metadata.plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘useful-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ComputeHartigan
> ### Title: Compute Hartigan's Number
> ### Aliases: ComputeHartigan
> ### Keywords: cluster clustering hartigan kmeans
> 
> ### ** Examples
> 
> data(iris)
> hartiganResults <- FitKMeans(iris[, -ncol(iris)])
> PlotHartigan(hartiganResults)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘userfriendlyscience-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: associationsDiamondPlot
> ### Title: A diamondplot with confidence intervals for associations
> ### Aliases: associationsDiamondPlot associationsToDiamondPlotDf
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ### Simple diamond plot with correlations
> ### and their confidence intervals
> 
> associationsDiamondPlot(mtcars,
+                         covariates=c('cyl', 'hp', 'drat', 'wt',
+                                      'am', 'gear', 'vs', 'carb', 'qsec'),
+                         criteria='mpg');
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_sources_and_cleaning.Rmd’ using rmarkdown
--- finished re-building ‘Data_sources_and_cleaning.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Loading required package: usfertilizer
Loading required package: tidyverse
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 53-67 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘usmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: .east_north_central
> ### Title: East North Central census division
> ### Aliases: .east_north_central
> ### Keywords: datasets
> 
> ### ** Examples
> 
> plot_usmap(include = .east_north_central, labels = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 21-22 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘mapping.Rmd’ using rmarkdown
Quitting from lines 21-27 (mapping.Rmd) 
Error: processing vignette 'mapping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mapping.Rmd’

SUMMARY: processing the following files failed:
  ‘introduction.Rmd’ ‘mapping.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Running examples in ‘valr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bed_closest
> ### Title: Identify closest intervals.
> ### Aliases: bed_closest
> 
> ### ** Examples
> 
> x <- trbl_interval(
+   ~chrom, ~start, ~end,
+   'chr1', 100,    125
+ )
> 
> y <- trbl_interval(
+   ~chrom, ~start, ~end,
+   'chr1', 25,     50,
+   'chr1', 140,    175
+ )
> 
> bed_glyph(bed_closest(x, y))
Error in Summary.unit(c(4.8, 4.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘valr.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 124-136 (valr.Rmd) 
Error: processing vignette 'valr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘valr.Rmd’

SUMMARY: processing the following file failed:
  ‘valr.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 289-294 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  ── 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  ── 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ───────────────
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘vanquish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary_vcf
> ### Title: VCF Data Summary
> ### Aliases: summary_vcf
> 
> ### ** Examples
> 
> data("vcf_example")
> tmp <- summary_vcf(vcf = vcf_example, ZG = 'het', CHR = c(1,2))
> plot(tmp$scatter)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘varian-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vmp_plot
> ### Title: Plot the posterior distributions of the focal parameters from a
> ###   VM model
> ### Aliases: vmp_plot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # Using made up data because the real models take a long time to run
> set.seed(1234) # make reproducible
> vmp_plot(matrix(rnorm(1000), ncol = 2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: vmp_plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘VarSelLCM.Rmd’ using rmarkdown
Quitting from lines 96-97 (VarSelLCM.Rmd) 
Error: processing vignette 'VarSelLCM.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘VarSelLCM.Rmd’

SUMMARY: processing the following file failed:
  ‘VarSelLCM.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vcdExtra-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cormorants
> ### Title: Advertising Behavior by Males Cormorants
> ### Aliases: Cormorants
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Cormorants)
> str(Cormorants)
'data.frame':	343 obs. of  8 variables:
 $ category   : Ord.factor w/ 3 levels "Pre"<"Incubation"<..: 1 1 1 1 1 1 1 1 1 1 ...
 $ week       : int  1 1 1 1 1 1 1 1 1 1 ...
 $ station    : Factor w/ 6 levels "B1","B2","C1",..: 3 3 3 3 3 3 3 4 4 4 ...
 $ nest       : Ord.factor w/ 3 levels "no"<"partial"<..: 1 1 2 2 2 3 3 1 1 1 ...
 $ height     : Ord.factor w/ 3 levels "low"<"mid"<"high": 2 3 2 3 3 2 3 2 2 3 ...
 $ density    : Ord.factor w/ 4 levels "zero"<"few"<"moderate"<..: 2 2 2 2 2 2 2 2 2 2 ...
 $ tree_health: Factor w/ 2 levels "dead","healthy": 2 2 2 2 1 2 2 2 1 2 ...
 $ count      : int  3 2 2 2 1 3 3 1 8 3 ...
> 
> library(ggplot2)
> ggplot(Cormorants, aes(count)) + geom_histogram(binwidth=0.5) + 
+ 	labs(x="Number of birds advertising")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vcd-tutorial.Rnw’ using Sweave
Loading required package: vcd
Loading required package: grid
Loading required package: gnm
The following objects are masked _by_ .GlobalEnv:

    A, B, C

Error: processing vignette 'vcd-tutorial.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vcd-tutorial.Rnw’

SUMMARY: processing the following file failed:
  ‘vcd-tutorial.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vcrpart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fvcm
> ### Title: Bagging and Random Forests based on 'tvcm'
> ### Aliases: fvcm fvcm_control fvcolmm fvcolmm_control fvcglm
> ###   fvcglm_control
> ### Keywords: models
> 
> ### ** Examples
> 
> ## ------------------------------------------------------------------- #
> ## Dummy example:
> ##
> ## Bagging 'tvcm' on the artificially generated data 'vcrpart_3'. The 
> ## true coefficient function is a sinus curve between -pi/2 and pi/2. 
> ## The parameters 'maxstep = 3' and 'K = 5' are chosen to restrict the 
> ## computations.
> ## ------------------------------------------------------------------- #
> 
> ## simulated data
> data(vcrpart_3)
> 
> ## setting parameters
> control <-
+   fvcm_control(maxstep = 3, 
+                folds = folds_control("subsampling", K = 5, 0.5, seed = 3))
> 
> ## fitting the forest
> model <- fvcm(y ~ vc(z1, by = x1), data = vcrpart_3, 
+               family = gaussian(), control = control)
* fitting an initial tree ... OK
[ 2 ][ 1 ][ 4 ][ 3 ][ 5 ]
> 
> ## plot the first two trees
> plot(model, "coef", 1:2)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Running examples in ‘VDAP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aaDist
> ### Title: Position Independent Amino Acid Distributions
> ### Aliases: aaDist
> ### Keywords: ~distributions ~composition
> 
> ### ** Examples
> 
> protEx <- data.frame(Peptides = c("PWRGPWARVGSG","GYNRVGQGSG","PWRGPWARVGSG","GYNRVGQGSG","GSG"))
> 
> ## Plot example with GSG linker ##
> 
> aaDistEx <- aaDist(protEx,"aaDistEx Plot",linker = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: aaDist ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘vdg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.spv
> ### Title: Plot VDGs or FDS plots
> ### Aliases: plot.spv plot.spvforlist plot.spvlist plot.spvlistforlist
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> # Single design (class 'spv')
> # Larger n should be used in actual cases
> library(rsm)
> bbd3 <- as.data.frame(bbd(3)[,3:5])
> colnames(bbd3) <- paste0("x", 1:3)
> quad.3f <- formula(~ x1*x2*x3 - x1:x2:x3 + I(x1^2) + I(x2^2) + I(x3^2))
> set.seed(1234)
> out <- spv(n = 1000, design = bbd3, type = "spherical", formula = quad.3f)
> out

Object of class 'spv'

Call:
spv.data.frame(n = 1000, design = bbd3, type = "spherical", formula = quad.3f)

Sample dimensions:
1000 columns and 3 rows

Design space type:
Cuboidal

Summary of Scaled Prediction Variance (SPV):
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  3.632   6.238  11.950  12.951  18.638  32.782 
> plot(out)
Plot 5 = 'boxplots' cannot be produced: 'at' is FALSE
$fds
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vdg.Rnw’ using knitr
Quitting from lines 239-245 (vdg.Rnw) 
Error: processing vignette 'vdg.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vdg.Rnw’

SUMMARY: processing the following file failed:
  ‘vdg.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vdmR-vignette.Rnw’ using knitr
Quitting from lines 40-42 (vdmR-vignette.Rnw) 
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vdmR-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘vdmR-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘abalone-example.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 135-136 (abalone-example.Rmd) 
Error: processing vignette 'abalone-example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘abalone-example.Rmd’

--- re-building ‘bike-rental.Rmd’ using rmarkdown
Loading required package: SparseM

Attaching package: 'SparseM'

The following object is masked from 'package:base':

    backsolve


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: 'scales'

The following object is masked from 'package:purrr':

    discard

Quitting from lines 89-97 (bike-rental.Rmd) 
Error: processing vignette 'bike-rental.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bike-rental.Rmd’

SUMMARY: processing the following files failed:
  ‘abalone-example.Rmd’ ‘bike-rental.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘methodComparison.Rnw’ using Sweave
Loading required package: sm
Package 'sm', version 2.2-5.6: type help(sm) for summary information
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

--- finished re-building ‘methodComparison.Rnw’

--- re-building ‘usageExamples.Rnw’ using Sweave
Loading required package: ggplot2
Error: processing vignette 'usageExamples.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usageExamples.Rnw’

SUMMARY: processing the following file failed:
  ‘usageExamples.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vip-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vi
> ### Title: Variable Importance
> ### Aliases: vi
> 
> ### ** Examples
> 
> #
> # A projection pursuit regression example
> #
> 
> # Load the sample data
> data(mtcars)
> 
> # Fit a projection pursuit regression model
> mtcars.ppr <- ppr(mpg ~ ., data = mtcars, nterms = 1)
> 
> # Compute variable importance scores
> vi(mtcars.ppr, method = "ice")
Warning: Setting `method = "ice"` is experimental, use at your own risk!
# A tibble: 10 x 2
   Variable Importance
   <chr>         <dbl>
 1 wt           3.44  
 2 hp           2.57  
 3 gear         1.85  
 4 qsec         1.56  
 5 cyl          0.743 
 6 am           0.690 
 7 vs           0.448 
 8 drat         0.245 
 9 carb         0.0870
10 disp         0.0248
> 
> # Plot variable importance scores
> vip(mtcars.ppr, method = "ice")
Warning: Setting `method = "ice"` is experimental, use at your own risk!
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
> library(hexbin)
> 
> dat <- data.frame(x = rnorm(10000), y = rnorm(10000))
> 
> ggplot(dat, aes(x = x, y = y)) +
+   geom_hex() + coord_fixed() +
+   scale_fill_gradientn(colours = viridis(256, option = "D"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘viridis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_viridis
> ### Title: Viridis color scales
> ### Aliases: scale_color_viridis scale_colour_viridis scale_color_viridis
> ###   scale_fill_viridis
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # ripped from the pages of ggplot2
> p <- ggplot(mtcars, aes(wt, mpg))
> p + geom_point(size=4, aes(colour = factor(cyl))) +
+     scale_color_viridis(discrete=TRUE) +
+     theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-viridis.Rmd’ using rmarkdown
Quitting from lines 55-59 (intro-to-viridis.Rmd) 
Error: processing vignette 'intro-to-viridis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-to-viridis.Rmd’

SUMMARY: processing the following file failed:
  ‘intro-to-viridis.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘visdat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vis_compare
> ### Title: Visually compare two dataframes and see where they are
> ###   different.
> ### Aliases: vis_compare
> 
> ### ** Examples
> 
> 
> # make a new dataset of iris that contains some NA values
> aq_diff <- airquality
> aq_diff[1:10, 1:2] <- NA
> vis_compare(airquality, aq_diff)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(visdat)
  > 
  > test_check("visdat")
  3.1.0FreeType version: 2.9.1
  ── 1. Error: vis_guess creates the right plot (@test-vis-guess.R#10)  ──────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: vdiffr::expect_doppelganger("vis_guess vanilla", vis_guess_plot) at testthat/test-vis-guess.R:10
  2: writer(fig, testcase, title)
  3: print_plot(plot, title)
  4: print_plot.ggplot(plot, title)
  5: print(p)
  6: print.ggplot(p)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  nrows =  1000 ncols =  1000══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 38 SKIPPED: 6 FAILED: 1
  1. Error: vis_guess creates the right plot (@test-vis-guess.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_visdat.Rmd’ using rmarkdown
Quitting from lines 60-63 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_visdat.Rmd’

SUMMARY: processing the following file failed:
  ‘using_visdat.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vistributions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vdist_binom_plot
> ### Title: Visualize binomial distribution
> ### Aliases: vdist_binom_plot vdist_binom_prob vdist_binom_perc
> 
> ### ** Examples
> 
> # visualize binomial distribution
> vdist_binom_plot(10, 0.3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-vistributions.Rmd’ using rmarkdown
Quitting from lines 44-45 (introduction-to-vistributions.Rmd) 
Error: processing vignette 'introduction-to-vistributions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-vistributions.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-vistributions.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vmd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vmd
> ### Title: Create VMD Object
> ### Aliases: R6Vmd as.data.frame.vmd plot.vmd vmd
> ### Keywords: datasets
> 
> ### ** Examples
> 
> x = seq(-2*pi,2*pi,length.out=1000)
> signal = cos(x)
> v = vmd(signal,DC=FALSE,tol=1e-3)
> v$getResult()
> plot(v)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-volleystat.Rmd’ using rmarkdown
Quitting from lines 74-78 (Introduction-to-volleystat.Rmd) 
Error: processing vignette 'Introduction-to-volleystat.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction-to-volleystat.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-volleystat.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘voteogram-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: house_carto
> ### Title: Produce a ProPublica- or GovTrack-style House roll call vote
> ###   cartogram
> ### Aliases: house_carto
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # what you'd normally do
> ##D rep <- roll_call("house", 115, 1, 256)
> ## End(Not run)
> 
> # using a saved object
> rep <- readRDS(system.file("extdata", "rep.rds", package="voteogram"))
> 
> house_carto(rep, pp_square=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_voteogram.Rmd’ using rmarkdown
Quitting from lines 65-68 (intro_to_voteogram.Rmd) 
Error: processing vignette 'intro_to_voteogram.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_to_voteogram.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_to_voteogram.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘vpc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: new_vpc_theme
> ### Title: Create a customized VPC theme
> ### Aliases: new_vpc_theme
> 
> ### ** Examples
> 
> theme1 <- new_vpc_theme(update = list(
+   obs_color = "red",
+   obs_ci_color = "#aa0000",
+   obs_alpha = .3,
+   sim_pi_fill = "#cc8833",
+   sim_pi_size = 2
+ ))
> vpc(simple_data$sim, simple_data$obs, vpc_theme = theme1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘test-add_sim_index_number.R’ [3s/4s]
  Running ‘test-filter_dv.R’ [0s/0s]
  Running ‘test-labeller.R’ [5s/5s]
  Running ‘test-softwaretype.R’ [0s/1s]
  Running ‘test-strat-col-detection.R’ [0s/1s]
  Running ‘test-vpc.R’ [4s/5s]
  Running ‘test-vpc_cat.R’ [2s/2s]
  Running ‘test-vpc_cens.R’ [8s/8s]
  Running ‘test-vpc_tte.R’ [8s/9s]
Running the tests in ‘tests/test-vpc_cens.R’ failed.
Complete output:
  > library(vpc)
  > library(testit)
  > Sys.setenv("R_TESTS" = "")
  > 
  > ## Test regular vpc in presence of lloq / uloq data
  > obj1 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, uloq = 120, vpcdb = TRUE)
  > obj2 <- vpc(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 20, vpcdb = TRUE)
  > assert("6 values in upper percentile flagged as >uloq", vpc:::is_equal(sum(is.na(obj1$aggr_obs$obs95)), 6))
  > assert("4 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs5)), 4))
  > assert("1 values in upper percentile flagged as <lloq", vpc:::is_equal(sum(is.na(obj2$aggr_obs$obs50)), 1))
  > 
  > ## test vpc func
  > obj <- vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 30, vpcdb = TRUE)
  > vpc_cens(sim = vpc::simple_data$sim, obs = vpc::simple_data$obs, lloq = 30)
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
  Execution halted
Running examples in ‘vqtl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.scanonevar
> ### Title: plot.scanonevar
> ### Aliases: plot.scanonevar
> 
> ### ** Examples
> 
> set.seed(27599)
> test.cross <- qtl::sim.cross(map = qtl::sim.map(len = rep(20, 3), n.mar = 5), n.ind = 50)
> test.sov <- scanonevar(cross = test.cross)
calculating genoprobs with stepwidth = 5, off.end = 0, error.prob = 1e-4, map.function = 'haldane'
> plot(x = test.sov)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘vrcp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vrcp
> ### Title: Estimation for Varying Regression Segments and Change Point in
> ###   Heteroscedastic Data
> ### Aliases: vrcp
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Test the vrcp() using simulated data sets
> 
> # Example 1: L-L model with "c0", continuity at change point and common variance
> # Simulate the data
> x1<-seq(0,2,by=0.05)
> x2<-seq(2.05,5,by=0.05)
> 
> # The true regression functions
> yt1 <- 2+0.5*x1
> yt2 <- -1+2*x2
> 
> # Add noises
> y1<-yt1+rnorm(length(x1),0,0.25)
> y2<- yt2+rnorm(length(x2),0,0.25)
> z<-data.frame(c(x1,x2),c(y1,y2))
> names(z)=c("x","y")
> 
> # z is the simulated data in data frame. Let's visualize it
> plot(z)
> 
> # It looks like a L-L regression with a change point between 1.5 and 2.5
> # Fit with vrcp with L-L segments and "c0" constraint
> ans <- vrcp(z,1.5,2.5,"c0","L","L","Common", spline = "TRUE") # Fit with common variance
> ans
$maxloglik
[1] 8.424511

$sigma2
[1] 0.04955366

$coe
[1]  2.0477449  0.4710914 -0.8869335  1.9760547

$changepoint
[1] 1.95

$plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: GenomicRanges
Loading required package: stats4
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, 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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Quitting from lines 74-84 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘walker.Rmd’ using rmarkdown
Quitting from lines 76-78 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘walker.Rmd’

SUMMARY: processing the following file failed:
  ‘walker.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘walrus-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rplots
> ### Title: Box & Violin Plots
> ### Aliases: rplots
> 
> ### ** Examples
> 
> data('eurosoccer', package='WRS2')
> 
> # violin plots
> 
> walrus::rplots(
+     data = eurosoccer,
+     vars = "GoalsGame",
+     splitBy = "League")

 BOX & VIOLIN PLOTS
Loading required namespace: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... <Anonymous> -> <Anonymous> -> eval -> eval -> <Anonymous>
Execution halted
Running examples in ‘warbleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coor.graph
> ### Title: Coordinated singing graphs
> ### Aliases: coor.graph
> 
> ### ** Examples
> 
> {
+ 
+ # First set temporary folder
+ # setwd(tempdir())
+ 
+ # load simulate singing events  (see data documentation)
+ data(sim.coor.sing)
+ 
+ # make coor.graphs in tiff format
+ coor.graph(X = sim.coor.sing, ovlp = TRUE, only.coor = FALSE, xl =2, res =80, 
+ it = "tiff", img = TRUE)
+ 
+ 
+ #' # make coor.graphs in graphic device format
+ cgs <- coor.graph(X = sim.coor.sing, ovlp = TRUE, only.coor = FALSE, img = FALSE)
+ 
+ cgs
+ }

   |                                                  | 0 % ~calculating  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: coor.graph ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics

Execution halted
Running examples in ‘waterfalls-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: waterfall
> ### Title: Create waterfall charts
> ### Aliases: waterfall
> 
> ### ** Examples
> 
> waterfall(values = round(rnorm(5), 1), labels = letters[1:5], calc_total = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Wats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CartesianPeriodic
> ### Title: Linear Plot with Periodic Elements
> ### Aliases: CartesianPeriodic
> ### Keywords: Cartesian
> 
> ### ** Examples
> 
> library(Wats) #Load the package
> changeMonth <- base::as.Date("1996-02-15")
> dsLinear <- CountyMonthBirthRate2005Version
> dsLinear <- dsLinear[dsLinear$CountyName=="oklahoma", ]
> dsLinear <- AugmentYearDataWithMonthResolution(dsLinear=dsLinear, dateName="Date")
> hSpread <- function( scores ) { return( quantile(x=scores, probs=c(.25, .75)) ) }
> portfolio <- AnnotateData(
+     dsLinear,
+     dvName = "BirthRate",
+     centerFunction = median,
+     spreadFunction = hSpread
+ )
> 
> CartesianPeriodic(
+   portfolio$dsLinear,
+   portfolio$dsPeriodic,
+   xName = "Date",
+   yName = "BirthRate",
+   stageIDName = "StageID",
+   changePoints = changeMonth,
+   changePointLabels = "Bombing Effect"
+ )
Warning: Ignoring unknown aesthetics: y
Warning: Ignoring unknown aesthetics: y
Warning: Ignoring unknown aesthetics: y
Warning: Ignoring unknown aesthetics: y
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MbrFigures.Rmd’ using knitr
Quitting from lines 103-124 (MbrFigures.Rmd) 
Error: processing vignette 'MbrFigures.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MbrFigures.Rmd’

--- re-building ‘OkFertilityWithIntercensalEstimates.Rmd’ using knitr
Quitting from lines 96-154 (OkFertilityWithIntercensalEstimates.Rmd) 
Error: processing vignette 'OkFertilityWithIntercensalEstimates.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘OkFertilityWithIntercensalEstimates.Rmd’

SUMMARY: processing the following files failed:
  ‘MbrFigures.Rmd’ ‘OkFertilityWithIntercensalEstimates.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_the_wbstats_package.Rmd’ using rmarkdown
Quitting from lines 193-201 (Using_the_wbstats_package.Rmd) 
Error: processing vignette 'Using_the_wbstats_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using_the_wbstats_package.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_the_wbstats_package.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘flags.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

--- finished re-building ‘flags.Rmd’

--- re-building ‘glossary.Rmd’ using rmarkdown
--- finished re-building ‘glossary.Rmd’

--- re-building ‘interpolate_data.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 47-56 (interpolate_data.Rmd) 
Error: processing vignette 'interpolate_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interpolate_data.Rmd’

--- re-building ‘weathercan.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 104-108 (weathercan.Rmd) 
Error: processing vignette 'weathercan.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘weathercan.Rmd’

SUMMARY: processing the following files failed:
  ‘interpolate_data.Rmd’ ‘weathercan.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘webr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.htest
> ### Title: Plotting distribution of statistic for object "htest"
> ### Aliases: plot.htest
> 
> ### ** Examples
> 
> 
> require(moonBook)
Loading required package: moonBook
> require(webr)
> ## chi-square test
> x=chisq.test(table(mtcars$am,mtcars$cyl))
Warning in chisq.test(table(mtcars$am, mtcars$cyl)) :
  Chi-squared approximation may be incorrect
> plot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-htest.Rmd’ using rmarkdown
Loading required package: moonBook
Loading required package: webr
Quitting from lines 37-44 (plot-htest.Rmd) 
Error: processing vignette 'plot-htest.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plot-htest.Rmd’

SUMMARY: processing the following file failed:
  ‘plot-htest.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Life_Data_Analysis_Part_I.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Quitting from lines 59-75 (Life_Data_Analysis_Part_I.Rmd) 
Error: processing vignette 'Life_Data_Analysis_Part_I.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Life_Data_Analysis_Part_I.Rmd’

--- re-building ‘Life_Data_Analysis_Part_II.Rmd’ using rmarkdown
Loading required package: survival
Loading required package: nlme
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

--- finished re-building ‘Life_Data_Analysis_Part_II.Rmd’

--- re-building ‘Life_Data_Analysis_Part_III.Rmd’ using rmarkdown
--- finished re-building ‘Life_Data_Analysis_Part_III.Rmd’

SUMMARY: processing the following file failed:
  ‘Life_Data_Analysis_Part_I.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘WeightedROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WeightedROC
> ### Title: WeightedROC
> ### Aliases: WeightedROC
> 
> ### ** Examples
> 
> 
> ## WeightedROC can compute ROC curves for data sets with variable
> ## weights.
> library(WeightedROC)
> y <- c(-1, -1, 1, 1, 1)
> w <- c(1, 1, 1, 4, 5)
> y.hat <- c(1, 2, 3, 1, 1)
> tp.fp <- WeightedROC(y.hat, y, w)
> if(require(ggplot2)){
+   gg <- ggplot()+
+     geom_path(aes(FPR, TPR), data=tp.fp)+
+     coord_equal()
+   print(gg)
+ }else{
+   plot(TPR~FPR, tp.fp, type="l")
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Definition.Rnw’ using Sweave
Error: processing vignette 'Definition.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Definition.Rnw’

--- re-building ‘Speed.Rnw’ using Sweave
Loading required package: ElemStatLearn
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: microbenchmark
Loading required package: PRROC
Loading required package: WeightedROC
Loading required package: ROCR
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Loading required package: pROC
Type 'citation("pROC")' for a citation.

Attaching package: ‘pROC’

The following object is masked from ‘package:glmnet’:

    auc

The following objects are masked from ‘package:stats’:

    cov, smooth, var

Loading required package: ggplot2

Error: processing vignette 'Speed.Rnw' failed with diagnostics:
 chunk 4 (label = test-ROC-curves) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘Speed.Rnw’

SUMMARY: processing the following files failed:
  ‘Definition.Rnw’ ‘Speed.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘wevid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotWdists
> ### Title: Plot the distribution of the weight of evidence in cases and in
> ###   controls
> ### Aliases: plotWdists
> 
> ### ** Examples
> 
> data(cleveland)
> densities <- with(cleveland, Wdensities(y, posterior.p, prior.p))
> plotWdists(densities)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘who_vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 64-80 (who_vignette.Rmd) 
Error: processing vignette 'who_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘who_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘who_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘widyr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: widely_svd
> ### Title: Turn into a wide matrix, perform SVD, return to tidy form
> ### Aliases: widely_svd widely_svd_
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

> library(gapminder)
> 
> # principal components driving change
> gapminder_svd <- gapminder %>%
+   widely_svd(country, year, lifeExp)
> 
> gapminder_svd
# A tibble: 1,704 x 3
   country     dimension   value
   <fct>           <int>   <dbl>
 1 Afghanistan         1 -0.0522
 2 Albania             1 -0.0949
 3 Algeria             1 -0.0824
 4 Angola              1 -0.0526
 5 Argentina           1 -0.0955
 6 Australia           1 -0.103 
 7 Austria             1 -0.101 
 8 Bahrain             1 -0.0913
 9 Bangladesh          1 -0.0696
10 Belgium             1 -0.102 
# … with 1,694 more rows
> 
> # compare SVDs, join with other data
> library(ggplot2)
> library(tidyr)
> 
> gapminder_svd %>%
+   spread(dimension, value) %>%
+   inner_join(distinct(gapminder, country, continent), by = "country") %>%
+   ggplot(aes(`1`, `2`, label = country)) +
+   geom_point(aes(color = continent)) +
+   geom_text(vjust = 1, hjust = 1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
--- finished re-building ‘intro.Rmd’

--- re-building ‘united_nations.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

If you use data from the unvotes package, please cite the following:

Erik Voeten "Data and Analyses of Voting in the UN General Assembly" Routledge Handbook of International Organization, edited by Bob Reinalda (published May 27, 2013)
Warning in countrycode(item2, "country.name", "iso2c") :
  Some values were not matched unambiguously: Czechoslovakia, German Democratic Republic, Yemen Arab Republic, Yemen People's Republic, Yugoslavia, Zanzibar

Quitting from lines 81-92 (united_nations.Rmd) 
Error: processing vignette 'united_nations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘united_nations.Rmd’

SUMMARY: processing the following file failed:
  ‘united_nations.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wikisourcer.Rmd’ using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 58-69 (wikisourcer.Rmd) 
Error: processing vignette 'wikisourcer.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wikisourcer.Rmd’

SUMMARY: processing the following file failed:
  ‘wikisourcer.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘windfarmGA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotWindrose
> ### Title: Plot a Windrose
> ### Aliases: plotWindrose
> 
> ### ** Examples
> 
> ## Exemplary Input Wind speed and direction data frame
> # Uniform wind speed and single wind direction
> data.in <- data.frame(ws = 12, wd = 0)
> windrosePlot <- plotWindrose(data = data.in, spd = data.in$ws,
+    dir = data.in$wd)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotWindrose ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordbankr.Rmd’ using rmarkdown
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Warning in .local(conn, statement, ...) :
  Decimal MySQL column 6 imported as numeric
Quitting from lines 76-86 (wordbankr.Rmd) 
Error: processing vignette 'wordbankr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wordbankr.Rmd’

SUMMARY: processing the following file failed:
  ‘wordbankr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘WordR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addPlots
> ### Title: Read Word document with bookmarks and create other Word document
> ###   with rendered plots in place.
> ### Aliases: addPlots
> 
> ### ** Examples
> 
> library(ggplot2)
> Plots<-list(plot1=function()plot(hp~wt,data=mtcars,col=cyl),
+  plot2=function()print(ggplot(mtcars,aes(x=wt,y=hp,col=as.factor(cyl)))+geom_point()))
> addPlots(
+  paste(examplePath(),'templates/templatePlots.docx',sep = ''),
+  paste(tempdir(),'/resultPlots.docx',sep = ''),
+  Plots,height=4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: addPlots ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wql-package.Rmd’ using rmarkdown
Quitting from lines 96-97 (wql-package.Rmd) 
Error: processing vignette 'wql-package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wql-package.Rmd’

SUMMARY: processing the following file failed:
  ‘wql-package.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘WRTDStidal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dynaplot
> ### Title: Plot model response to salinity or flow as a lineplot for all
> ###   months
> ### Aliases: dynaplot dynaplot.tidal dynaplot.tidalmean
> 
> ### ** Examples
> 
> 
> # load a fitted tidal object
> data(tidfit)
> 
> # plot using defaults, 
> # defaults to the fiftieth quantile for all years
> dynaplot(tidfit)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘WVPlots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BinaryYScatterPlot
> ### Title: Plot a scatter plot of a binary variable with smoothing curve.
> ### Aliases: BinaryYScatterPlot
> 
> ### ** Examples
> 
> 
> set.seed(34903490)
> x = rnorm(50)
> y = 0.5*x^2 + 2*x + rnorm(length(x))
> frm = data.frame(x=x,y=y,yC=y>=as.numeric(quantile(y,probs=0.8)))
> frm$absY <- abs(frm$y)
> frm$posY = frm$y > 0
> frm$costX = 1
> WVPlots::BinaryYScatterPlot(frm, "x", "posY",
+    title="Example 'Probability of Y' Plot")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘package_test_runner.R’ [4s/4s]
Running the tests in ‘tests/package_test_runner.R’ failed.
Complete output:
  > 
  > # package to check
  > pkg = "WVPlots"
  > 
  > # This file is distributed without license requirements, feel free to alter/copy.
  > if(requireNamespace("RUnit", quietly = TRUE) &&
  +    requireNamespace("wrapr", quietly = TRUE)) {
  +   # library("RUnit") # uncomment this if you want RUnit attached during testing
  +   library(pkg, character.only = TRUE)
  +   wrapr::run_package_tests(pkg, verbose = TRUE, require_RUnit_attached = FALSE)
  + }
  [1] "RUnit testing package WVPlots version 1.0.9"
  
  
  Executing test function test_a_1  ... Timing stopped at: 0.234 0.043 0.326
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
   done successfully.
  
  
  
  Executing test function test_a_2  ... Timing stopped at: 0.615 0.025 0.833
  Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
   done successfully.
  
  RUNIT TEST PROTOCOL -- Fri Mar 29 19:43:02 2019 
  *********************************************** 
  Number of test functions: 2 
  Number of errors: 2 
  Number of failures: 0 
  
   
  1 Test Suite : 
  WVPlots unit tests - 2 test functions, 2 errors, 0 failures
  ERROR in test_a_1: Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  ERROR in test_a_2: Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
    VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Error in wrapr::run_package_tests(pkg, verbose = TRUE, require_RUnit_attached = FALSE) : 
    package WVPlots had test failures/errors
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘WVPlots_concept.Rmd’ using rmarkdown
Quitting from lines 21-24 (WVPlots_concept.Rmd) 
Error: processing vignette 'WVPlots_concept.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘WVPlots_concept.Rmd’

--- re-building ‘WVPlots_examples.Rmd’ using rmarkdown
Quitting from lines 32-33 (WVPlots_examples.Rmd) 
Error: processing vignette 'WVPlots_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘WVPlots_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘WVPlots_concept.Rmd’ ‘WVPlots_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [51s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.061262 
  [1]	train-logloss:0.380601 
  [2]	train-logloss:0.247327 
  [3]	train-logloss:0.175046 
  [4]	train-logloss:0.122303 
  [5]	train-logloss:0.089890 
  [1]	train-logloss:0.497351 
  [2]	train-logloss:0.357289 
  [3]	train-logloss:0.257217 
  [4]	train-logloss:0.184524 
  [5]	train-logloss:0.132112 
  [1]	train-auc:0.900000	test-auc:0.800000 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	eval-error:0.042831	train-error:0.046522 
  [2]	eval-error:0.021726	train-error:0.022263 
  [1]	train-error:0.046522 
  [2]	train-error:0.022263 
  [1]	train-error:0.333333 
  ── 1. Error: xgb.plot.deepness works (@test_helpers.R#310)  ────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: xgb.ggplot.deepness(model = bst.Tree) at testthat/test_helpers.R:310
  2: multiplot(p1, p2, cols = 1)
  3: print(plots[[i]], vp = grid::viewport(layout.pos.row = matchidx$row, layout.pos.col = matchidx$col))
  4: print.ggplot(plots[[i]], vp = grid::viewport(layout.pos.row = matchidx$row, layout.pos.col = matchidx$col))
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 564 SKIPPED: 4 FAILED: 1
  1. Error: xgb.plot.deepness works (@test_helpers.R#310) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘xkcd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xkcdline
> ### Title: Draw lines or circunferences
> ### Aliases: xkcdline
> ### Keywords: manip
> 
> ### ** Examples
> 
> data <- data.frame(x1=c(1,2), y1=c(10,20), xend=c(2.5,0.5),
+ yend=c(20,10), model=c("low","high"))
> 
> ggplot() + xkcdline(mapping=aes(x=x1 +y1, y=y1, xend =xend, yend= yend,
+ color = model), data=data)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘XLConnect.Rnw’ using Sweave
Loading required package: XLConnect
Loading required package: XLConnectJars
XLConnect 0.2-15 by Mirai Solutions GmbH [aut],
  Martin Studer [cre],
  The Apache Software Foundation [ctb, cph] (Apache POI),
  Graph Builder [ctb, cph] (Curvesapi Java library)
http://www.mirai-solutions.com
https://github.com/miraisolutions/xlconnect
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/XLConnect/java/poi-ooxml-3.17.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper
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
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: ggplot2

Error: processing vignette 'XLConnect.Rnw' failed with diagnostics:
 chunk 20 (label = AdvancedExampleP5) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘XLConnect.Rnw’

--- re-building ‘XLConnectImpatient.Rnw’ using Sweave
--- finished re-building ‘XLConnectImpatient.Rnw’

SUMMARY: processing the following file failed:
  ‘XLConnect.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘xmR.Rmd’ using knitr

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 133-137 (xmR.Rmd) 
Error: processing vignette 'xmR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘xmR.Rmd’

SUMMARY: processing the following file failed:
  ‘xmR.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘xpose-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: amt_vs_idv
> ### Title: Compartment kinetics
> ### Aliases: amt_vs_idv
> 
> ### ** Examples
> 
> amt_vs_idv(xpdb_ex_pk)
Using data from $prob no.1
Tidying data by ID, SEX, MED1, MED2, AMT ... and 20 more variables
Error in Ops.unit(e2) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... f -> render_axis -> guide_axis -> Ops.unit -> Ops.unit
Execution halted
Running examples in ‘xray-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distributions
> ### Title: Analyze each variable and generate a histogram describing it's
> ###   distribution.
> ### Aliases: distributions
> 
> ### ** Examples
> 
> library(xray)
> distributions(mtcars)
================================================================================
Error in { : 
  task 1 failed - "VECTOR_ELT() can only be applied to a 'list', not a 'double'"
Calls: distributions -> %do% -> <Anonymous>
Execution halted
Running examples in ‘xsp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chiSqPeriodogramPlot
> ### Title: Draw a graph of chi-square periodogram
> ### Aliases: chiSqPeriodogramPlot
> 
> ### ** Examples
> 
> oscillation <- sin(seq(0, 2 * pi * 10, by = 2 * pi / 1440))
> oscillation.df <- data.frame(dateTime = 1:length(oscillation), value = oscillation)
> chiSqPeriodogramPlot(chiSqPeriodogram(oscillation.df))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ypr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adams_bt_03
> ### Title: Adams Lake Bull Trout Population Parameters
> ### Aliases: adams_bt_03
> ### Keywords: datasets
> 
> ### ** Examples
> 
> adams_bt_03
tmax: 20
k:    0.13
Linf: 131
t0:   0.2
Wb:   3.4
Ls:   40
Sp:   100
es:   1
Sm:   0
fb:   1
tR:   1
BH:   1
Rk:   3.8
M:    0.356674943938732
Mb:   0
Lv:   40
Vp:   5
Llo:  0
Lup:  131
Nc:   0
pi:   0.06
rho:  0
Hm:   0.15
Rmax: 1
A0:   0
Wa:   0.01
fa:   1
q:    0.1> ypr_plot_yield(adams_bt_03)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ypr.Rmd’ using rmarkdown
Quitting from lines 40-43 (ypr.Rmd) 
Error: processing vignette 'ypr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ypr.Rmd’

SUMMARY: processing the following file failed:
  ‘ypr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘YRmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pl.2tsgg
> ### Title: Time series plot for two variables with ggplot2
> ### Aliases: pl.2tsgg
> 
> ### ** Examples
> 
> DAX <- EuStockMarkets[,1]
> FTSE <- EuStockMarkets[,4]
> pl.2tsgg(DAX,FTSE, "Times Series Plot of DAX and FTSE", "Index")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘zebu.Rmd’ using rmarkdown
Quitting from lines 252-274 (zebu.Rmd) 
Error: processing vignette 'zebu.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘zebu.Rmd’

SUMMARY: processing the following file failed:
  ‘zebu.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: TSP
Loading required package: gtools
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, 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

Loading required package: grid
--- finished re-building ‘intro.Rmd’

--- re-building ‘selected_features.Rmd’ using rmarkdown
Quitting from lines 160-190 (selected_features.Rmd) 
Error: processing vignette 'selected_features.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘selected_features.Rmd’

SUMMARY: processing the following file failed:
  ‘selected_features.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘zoocat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmon_trans
> ### Title: Tools for plottin 'zoocat' objects with ggplot2
> ### Aliases: gmon_trans scale_x_gmon scale_y_gmon
> 
> ### ** Examples
> 
> library(ggplot2)
> df <- data.frame(month = gmon(-5:5), value = 1:11)
> ggplot(df, aes(month, value)) + 
+     geom_line() + geom_point() +
+     scale_x_gmon()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   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 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [3s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(alfred)
  > 
  > test_check("alfred")
  ── 1. Failure: Downloaded data is as expected (@test_download.R#29)  ───────────
  get_fred_series(...) not equal to data.frame(date = as.Date("2009-03-01"), test = 89.0085).
  Component "test": Mean relative difference: 8.425452e-05
  
  ── 2. Failure: Downloaded data is as expected (@test_download.R#36)  ───────────
  dplyr::filter(get_fred_series("INDPRO", "test"), date == "2009-03-01") not equal to data.frame(date = as.Date("2009-03-01"), test = 89.0085).
  Component "test": Mean relative difference: 8.425452e-05
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Downloaded data is as expected (@test_download.R#29) 
  2. Failure: Downloaded data is as expected (@test_download.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    help   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

The following object is masked from 'package:stats':

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
Execution halted
Package suggested but not available for checking: ‘qCBA’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    fontawesome-5.3.1   2.8Mb
    help                1.5Mb
Package suggested but not available for checking: ‘MonetDBLite’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
Packages suggested but not available for checking:
  ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> ### Name: write2
> ### Title: write2
> ### Aliases: write2 write2.arsenal_table write2.summary.arsenal_table
> ###   write2.comparedf write2.summary.comparedf write2.verbatim write2.yaml
> ###   write2.code.chunk write2.knitr_kable write2.xtable write2.character
> ###   write2.list write2.default
> 
> ### ** Examples
> 
> ## Not run: 
> ##D data(mockstudy)
> ##D # tableby example
> ##D tab1 <- tableby(arm ~ sex + age, data=mockstudy)
> ##D write2(tab1, tempfile(fileext = ".rtf"),
> ##D   toc = TRUE, # passed to rmarkdown::rtf_document, though in this case it's not practical
> ##D   quiet = TRUE, # passed to rmarkdown::render
> ##D   title = "My cool new title", # passed to summary.tableby
> ##D   output_format = rmarkdown::rtf_document)
> ## End(Not run)
> 
> write2html(list(
+   "# Header 1", # a header
+   code.chunk(a <- 1, b <- 2, a + b), # a code chunk
+   verbatim("hi there") # verbatim output
+ ),
+   tempfile(fileext = ".html"),
+   quite = TRUE)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Package suggested but not available for checking: ‘REBayes’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Package required but not available: ‘xgboost’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    java   7.5Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 33-35 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10011 milliseconds
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’ [29s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Failure: herdity and BAS (@test-bas-glm.R#420)  ──────────────────────────
  pima_BAS$probne0 not equal to pima_BAS_no$probne0.
  6/7 mismatches (average diff: 0.0696)
  [2] 0.11013 - 0.1136 == -3.47e-03
  [3] 1.00000 - 1.0000 == -2.54e-06
  [4] 0.63062 - 0.8284 == -1.98e-01
  [5] 0.02193 - 0.0220 == -1.03e-04
  [6] 0.00771 - 0.0101 == -2.42e-03
  [7] 0.31878 - 0.1051 ==  2.14e-01
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 150 SKIPPED: 0 FAILED: 1
  1. Failure: herdity and BAS (@test-bas-glm.R#420) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.3Mb
    libs   1.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   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.
Quitting from lines 2-14 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-14 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'graphical-ppcs.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
Running ‘testthat.R’ [20s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.7.1 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  1: bcgam(income ~ sm.incr(prestige, space = "E") + sm.conv(education) + type, data = duncan) at testthat/testthat.R:3
  2: bcgam.fit(y, xmat0, shapes0, zmat, nums0, ks0, sps0, nloop, burnin, family, xmatnms0, 
         znms)
  3: compileNimble(gaus)
  4: project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
  5: cppProj$compileFile(compileList, showCompilerOutput)
  6: compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
  7: compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Package suggested but not available for checking: ‘lumi’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
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 68-77 (bib2df.Rmd) 
Error: processing vignette 'bib2df.Rmd' failed with diagnostics:
Invalid URL: File is not readable.
Execution halted
Running examples in ‘bigdist-Ex.R’ failed
The error most likely occurred in:

> ### Name: bigdist
> ### Title: Read or Create a distance matrix on disk
> ### Aliases: bigdist
> 
> ### ** Examples
> 
> # basics of 'bigdist'
> # create a random matrix
> set.seed(1)
> amat <- matrix(rnorm(1e3), ncol = 10)
> td   <- tempdir()
> 
> # create a bigdist object with FBM (file-backed matrix) on disk
> temp <- bigdist(mat = amat, file = file.path(td, "temp_ex1"))
----
Location: /tmp/RtmptKay1Z/temp_ex1_100_float.bk
Size on disk: 0 GB
Computing distances ... 
Completed!
----
> temp
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp$fbm$backingfile
[1] "/tmp/RtmptKay1Z/temp_ex1_100_float.bk"
> temp$fbm[1, 2]
[1] 4.631341
> 
> # connect to FBM on disk as a bigdist object
> temp2 <- bigdist(file = file.path(td, "temp_ex1_100_float"))
> temp2
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp2$fbm[1,2]

 *** caught segfault ***
address fcbc0190, cause 'invalid permissions'

Traceback:
 1: extractMat(x$address, i, j)
 2: extract_matrix(x, transform_ind(i, n), transform_ind(j, m))
 3: temp2$fbm[1, 2]
 4: temp2$fbm[1, 2]
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$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]="webshot3963247790e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3963247790e.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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Package unavailable to check Rd xrefs: ‘bigrquery’
Installation failed.
See ‘/home/ripley/R/packages/tests32/bigrquery.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
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 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
Packages required but not available: ‘rcdk’ ‘ChemmineR’ ‘fmcsR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_scan
> ### Title: Example object of class 'scan'
> ### Aliases: example_scan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # get summary of example scan:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> 
> # example_scan was created with:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... is.odimfile -> h5ls -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
Running ‘testthat.R’ [11s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioRad)
  Welcome to bioRad version 0.4.0
  Warning: no running Docker daemon found Warning: bioRad functionality
  requiring Docker has been disabled
  
  To enable Docker functionality, start Docker and run 'check_docker()'
  in R
  > 
  > test_check("bioRad")
  ── 1. Error: Read a vertical profile (@test-read_vpfiles.R#5)  ─────────────────
  HDF5. File accessibilty. Unable to open file.
  1: expect_s3_class(readvp(vpfile), "vp") at testthat/test-read_vpfiles.R:5
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: readvp(vpfile)
  5: read_vpfiles(...)
  6: read_vp(files)
  7: is.vpfile(file)
  8: get_odim_object_type(file)
  9: is.odimfile(file)
  10: h5ls(file, recursive = FALSE)
  11: h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
  12: H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ── 2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13)  ────────
  HDF5. File accessibilty. Unable to open file.
  1: expect_is(readvp.list(c(vpfile, vpfile)), "list") at testthat/test-read_vpfiles.R:13
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: readvp.list(c(vpfile, vpfile))
  5: read_vpfiles(...)
  6: lapply(files, read_vp)
  7: FUN(X[[i]], ...)
  8: is.vpfile(file)
  9: get_odim_object_type(file)
  10: is.odimfile(file)
  11: h5ls(file, recursive = FALSE)
  12: h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
  13: H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 2
  1. Error: Read a vertical profile (@test-read_vpfiles.R#5) 
  2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Package suggested but not available for checking: ‘IHW’
Installation failed.
See ‘/home/ripley/R/packages/tests32/bliss.Rcheck/00install.out’ for details.
Package required but not available: ‘xgboost’

Package suggested but not available for checking: ‘bigrf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))
Running ‘testthat.R’ [445s/130s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blockForest)
  > 
  > test_check("blockForest")
  ── 1. Failure: Inbag counts match sample fraction, classification (@test_ranger.
  unique(colSums(inbag[51:100, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 2. Failure: Inbag counts match sample fraction, classification (@test_ranger.
  unique(colSums(inbag[101:150, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 3. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#8
  unique(colSums(inbag[51:100, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ── 4. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#9
  unique(colSums(inbag[101:150, ])) not equal to 45.
  1/1 mismatches
  [1] 44 - 45 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 405 SKIPPED: 0 FAILED: 4
  1. Failure: Inbag counts match sample fraction, classification (@test_ranger.R#71) 
  2. Failure: Inbag counts match sample fraction, classification (@test_ranger.R#80) 
  3. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#89) 
  4. Failure: Inbag counts match sample fraction, probability (@test_ranger.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward"),
+    k = 2))
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 2 1 2 2 2 2 2 2 2 1 1 2 1 1 1 1 1 2 2 2 

 *** caught segfault ***
address f52ec8, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/BMSC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Error: processing vignette 'BoolNet_package_vignette.Snw' failed with diagnostics:
 chunk 13 
Error in (function (interaction, index, gene)  : 
  No values for the "don't care" entries were specified for gene "Fkh2"!
Execution halted
Package suggested but not available for checking: ‘xgboost’
Package unavailable to check Rd xrefs: ‘xgboost’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
Warning in engine$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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   2.7Mb
Running ‘test-all.R’ [58s/90s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14)  ──────────────────
  object 'extra' not found
  1: oneway.test(extra ~ group, data = sleep) at testthat/test-stats-htest.R:14
  2: eval(m, parent.frame())
  3: eval(m, parent.frame())
  4: stats::model.frame(formula = extra ~ group, data = sleep)
  5: model.frame.default(formula = extra ~ group, data = sleep)
  6: eval(predvars, data, env)
  7: eval(predvars, data, env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 912 SKIPPED: 2 FAILED: 1
  1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   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.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'c3'

The following object is masked from 'package:dplyr':

    %>%

The following objects are masked from 'package:graphics':

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot45ab7b7e2019.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot45ab7b7e2019.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
Package which this enhances but not available for checking: ‘FastRWeb’
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Error 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.
CAST                   package:CAST                    R Documentation

'_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Supporting functionality to run 'caret' with spatial or
     spatial-temporal data. 'caret' is a frequently used package for
     model training and prediction using machine learning. This package
     includes functions to improve spatial-temporal modelling tasks
     using 'caret'. It prepares data for Leave-Location-Out and
     Leave-Time-Out cross-validation which are target-oriented
     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]="webshot25ad65854611.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot25ad65854611.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
Running examples in ‘cdcfluview-Ex.R’ failed
The error most likely occurred in:

> ### Name: age_group_distribution
> ### Title: Age Group Distribution of Influenza Positive Tests Reported by
> ###   Public Health Laboratories
> ### Aliases: age_group_distribution
> 
> ### ** Examples
> 
> agd <- age_group_distribution(years=2015)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: age_group_distribution ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘test-all.R’ [4s/19s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("cdcfluview")
  Loading required package: cdcfluview
  ── 1. Error: New API works (@test-cdcfluview.R#5)  ─────────────────────────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: expect_that(age_group_distribution(years = 2017), is_a("data.frame")) at testthat/test-cdcfluview.R:5
  2: condition(object)
  3: expect_is(x, class)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: age_group_distribution(years = 2017)
  7: httr::GET(url = "https://gis.cdc.gov/grasp/fluView6/GetFlu6AllDataP", httr::user_agent(.cdcfluview_ua), 
         httr::add_headers(Accept = "application/json, text/plain, */*", Referer = "https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html"), 
         httr::timeout(.httr_timeout))
  8: request_perform(req, hu$handle$handle)
  9: request_fetch(req$output, req$url, handle)
  10: request_fetch.write_memory(req$output, req$url, handle)
  11: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 1 FAILED: 1
  1. Error: New API works (@test-cdcfluview.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.8Mb
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [34s/44s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 834 SKIPPED: 0 FAILED: 1
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  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 object is masked from 'package:ClinReport':

    desc

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'nlme'

The following object is masked from 'package:dplyr':

    collapse

Loading required package: carData

Attaching package: 'car'

The following object is masked from 'package:dplyr':

    recode

Warning 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 60-71 (clinreport_modify_outputs.Rmd) 
Error: processing vignette 'clinreport_modify_outputs.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
Packages required but not available: ‘xcms’ ‘MSnbase’

Package suggested but not available for checking: ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘RWeka’
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 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
Package required but not available: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘cmpprocess-Ex.R’ failed
The error most likely occurred in:

> ### Name: cmpproc
> ### Title: COM Poisson Process Parameter Estimation.
> ### Aliases: cmpproc
> 
> ### ** Examples
> 
> ## Standard usage
> data(floodcount)
> cmpproc(floodcount$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 86-87 (codebook.Rmd) 
Error: processing vignette 'codebook.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Running examples in ‘coefplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract.coef.xgb.Booster
> ### Title: extract.coef.xgb.Booster
> ### Aliases: extract.coef.xgb.Booster
> 
> ### ** Examples
> 
> library(xgboost)
Error in library(xgboost) : there is no package called ‘xgboost’
Execution halted
Found the following significant warnings:
  "collapsed_lpcm.c", line 74: warning: improper pointer/integer combination: op ">"
See ‘/home/ripley/R/packages/tests32/collpcm.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(commonsMath)
  > 
  > test_check("commonsMath")
  Starting instance. ********************************
  Error in library(rscala) : there is no package called 'rscala'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  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 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
there is no package called 'rscala'
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    app   3.1Mb
    doc   2.4Mb
Package required but not available: ‘rminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigrquery’

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 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10003 milliseconds
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error 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 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   5.9Mb
Package which this enhances but not available for checking: ‘quanteda’
Package suggested but not available for checking: ‘quanteda’
Running examples in ‘corpustools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tCorpus$top_features
> ### Title: Show top features
> ### Aliases: tCorpus$top_features top_features
> 
> ### ** Examples
> 
> tc = tokens_to_tcorpus(corenlp_tokens, token_id_col = 'id')
> 
> tc$top_features('lemma')
Error in value[[3L]](cond) : 
  The dcast generic in data.table has been passed a data.frame (not a data.table) but the reshape2 package is not installed to process this type. Please either install reshape2 and try again, or pass a data.table to dcast instead.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘test-all.R’ [1s/19s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("crul")
  Loading required package: crul
  Error in curl::curl_fetch_memory(urls[i], handle = h) : 
    Timeout was reached: Operation timed out after 10000 milliseconds with 0 bytes received
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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:
there is no package called 'webshot'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    img   4.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    java  15.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
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:
there is no package called 'webshot'
Execution halted
Running examples in ‘dataone-Ex.R’ failed
The error most likely occurred in:

> ### Name: MNode
> ### Title: Create a MNode object representing a DataONE Member Node
> ###   repository.
> ### Aliases: MNode MNode,character-method MNode,D1Node-method
> 
> ### ** Examples
> 
> mn <- MNode("https://knb.ecoinformatics.org/knb/d1/mn/v2")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
Calls: MNode ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [64s/165s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("dataone")
  Loading required package: dataone
  ── 1. Error: auth_get (@test.auth_request.R#11)  ───────────────────────────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: xmlParse(content(dataone:::auth_get(uri, node = CNode()), as = "text")) at testthat/test.auth_request.R:11
  2: content(dataone:::auth_get(uri, node = CNode()), as = "text")
  3: stopifnot(is.response(x))
  4: withCallingHandlers(tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), 
         error = function(e) {
             e$call <- cl.i
             stop(e)
         }), warning = function(w) {
         w$call <- cl.i
         w
     })
  5: tryCatch(if (missE) ...elt(i) else eval(cl.i, envir = envir), error = function(e) {
         e$call <- cl.i
         stop(e)
     })
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 39 FAILED: 1
  1. Error: auth_get (@test.auth_request.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/data.table.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 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
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.
Running examples in ‘dbarts-Ex.R’ failed
The error most likely occurred in:

> ### Name: bart
> ### Title: Bayesian Additive Regression Trees
> ### Aliases: bart bart2 plot.bart predict.bart
> ### Keywords: nonparametric tree regression nonlinear
> 
> ### ** Examples
> 
> ## simulate data (example from Friedman MARS paper)
> ## y = f(x) + epsilon , epsilon ~ N(0, sigma)
> ## x consists of 10 variables, only first 5 matter
> 
> f <- function(x) {
+     10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+       10 * x[,4] + 5 * x[,5]
+ }
> 
> set.seed(99)
> sigma <- 1.0
> n     <- 100
> 
> x  <- matrix(runif(n * 10), n, 10)
> Ey <- f(x)
> y  <- rnorm(n, Ey, sigma)
> 
> ## run BART
> set.seed(99)
> bartFit <- bart(x, y)

Running BART with numeric y

number of trees: 200
Prior:
	k: 2.000000
	degrees of freedom in sigma prior: 3.000000
	quantile in sigma prior: 0.900000
	scale in sigma prior: 0.002181
	power and base for tree prior: 2.000000 0.950000
	use quantiles for rule cut points: false
data:
	number of training observations: 100
	number of test observations: 0
	number of explanatory variables: 10
	init sigma: 2.756573, curr sigma: 2.756573

Cutoff rules c in x<=c vs x>c
Number of cutoffs: (var: number of possible c):
(1: 100) (2: 100) (3: 100) (4: 100) (5: 100) 
(6: 100) (7: 100) (8: 100) (9: 100) (10: 100) 


 *** caught segfault ***
address bfa21bcc, cause 'memory not mapped'

Traceback:
 1: .Call(C_dbarts_run, ptr, as.integer(numBurnIn), as.integer(numSamples))
 2: sampler$run(0L, control@n.burn, FALSE)
 3: bart(x, y)
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$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


Attaching package: 'gridExtra'

The following object is masked from 'package:dplyr':

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Depends: includes the non-default packages:
  ‘Deducer’ ‘psych’ ‘GPArotation’ ‘mvnormtest’ ‘irr’ ‘klaR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

---------------------
Welcome to dendextend version 1.10.0
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


Attaching package: 'dendextend'

The following object is masked from 'package:stats':

    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  7.5Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.9Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’ ‘Rsymphony’
Running ‘test-that.R’ [98s/141s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  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  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
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.f [... truncated]
See ‘/home/ripley/R/packages/tests32/dgo.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    vignettes   3.4Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DMMF.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading dodgr
Re-compiling dodgr
Quitting from lines 18-19 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
System command error
Execution halted
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rmosek’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.9Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__f90_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 ‘__f90_esuw’, possibly from ‘write’ (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’
  Found ‘__f90_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 ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.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.
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-24
Package created on 2018-08-10

Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: nloptr
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: quadprog
Loading required package: earth
Loading required package: Formula
Loading required package: plotmo
Loading required package: plotrix
Loading required package: TeachingDemos
Loading required package: future
Quitting from lines 1049-1062 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot67f82067db6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot67f82067db6.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    appinformation  10.2Mb
    media            1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.2Mb
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: emxCholeskyComponent
> ### Title: Creates component for a Cholesky Model
> ### Aliases: emxCholeskyComponent
> 
> ### ** Examples
> 
>    
> # Create an ACE model in 22 lines
> require(EasyMx)
> require(OpenMx)
> data(twinData)
> twinVar = names(twinData)
> selVars <- c('ht1', 'bmi1','ht2','bmi2')
> mzdzData <- subset(twinData, zyg %in% c(1, 3), c(selVars, 'zyg'))
> mzdzData$RCoef <- c(1, NA, .5)[mzdzData$zyg]
> nVar = length(selVars)/2
> x <- paste0('x', 1:nVar)
> 
> acomp <- emxCholeskyComponent(x, 'A', hvalues=c(1, .5, 1), hlabels=c(NA, 'data.RCoef', NA))
> ccomp <- emxCholeskyComponent(x, 'C', hvalues=c(1, 1, 1))
> ecomp <- emxCholeskyComponent(x, 'E', hvalues=c(1, 0, 1))
> totalVar <- mxAlgebra(AKron + CKron + EKron, 'V', dimnames=list(selVars, selVars))
> totalMean <- emxMeans(selVars, type='twin')
> expect <- mxExpectationNormal(totalVar$name, totalMean$name)
> fitfun <- mxFitFunctionML()
> 
> comlist <- c(acomp, ccomp, ecomp, list(totalVar, totalMean, expect, fitfun))
> 
> model <- mxModel('model', comlist, mxData(mzdzData, 'raw'))
> run2 <- mxRun(model)
Running model with 11 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  Element-wise '+' not conformable: 'model.V arg 0' is 0x0 and 'model.EKron' is 4x4
model.V arg 0 =  matrix(c(    # 0x0), byrow=TRUE, nrow=0, ncol=0)
model.EKron =  matrix(c(    # 4x4
 0.639978, 1.57168,   0,   0
, 1.57168, 4.49979,   0,   0
,   0,   0, 0.639978, 1.57168
,   0,   0, 1.57168, 4.49979), byrow=TRUE, nrow=4, ncol=4)
Calls: mxRun -> runHelper
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
Running ‘testthat.r’ [2s/20s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("ecmwfr")
  Loading required package: ecmwfr
  Error in curl::curl_fetch_memory(url, handle = handle) : 
    Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  ── 1. Error: (unknown) (@test_ecmwf.r#40)  ─────────────────────────────────────
  $ operator is invalid for atomic vectors
  1: ecmwf_running(wf_server(service = "webapi")) at testthat/test_ecmwf.r:40
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 3 FAILED: 1
  1. Error: (unknown) (@test_ecmwf.r#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))

error: sort(): detected NaN
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9.5

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/RtmpZvaaUY"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc       4.9Mb
    extdata   5.3Mb
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 2-30 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
could not find function "pkg_ver"
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata  10.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    xsd   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   1.5Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: eNetXplorer
> ### Title: generates family of elastic net models for different alphas
> ### Aliases: eNetXplorer
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(75),ncol=3),y=rnorm(25),family="gaussian",
+ n_run=5,n_perm_null=4,alpha=c(0.5,1))
Error in if (any(lambda < 0)) stop("lambdas should be non-negative") : 
  missing value where TRUE/FALSE needed
Calls: eNetXplorer -> eNetXplorerGaussian -> glmnet
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.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
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Packages required but not available: ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    exiftool  14.4Mb
Package suggested but not available for checking: ‘tesseract’
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff at /home/ripley/R/packages/tests32/farff.Rcheck/tests/testthat/helper.R:17
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/107s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Error: The SSURGO inventory dataset is available at the correct URL (@test
  Timeout was reached: Operation timed out after 10086 milliseconds with 0 out of 0 bytes received
  1: expect_false(suppressWarnings(httr::http_error(url))) at testthat/test.SSURGO.R:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: suppressWarnings(httr::http_error(url))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: httr::http_error(url)
  7: http_error.character(url)
  8: http_error(HEAD(x, ...))
  9: HEAD(x, ...)
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  ── 2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURG
  `suppressWarnings(curl::curl(url) %>% readLines(n = 1))` threw an error.
  Message: Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 1 FAILED: 2
  1. Error: The SSURGO inventory dataset is available at the correct URL (@test.SSURGO.R#7) 
  2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURGO.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fedregs)
  > 
  > test_check("fedregs")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Space required after the Public Identifier [65]
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   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.

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).
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-49 (layout.Rmd) 
Error: processing vignette 'layout.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Package suggested but not available for checking: ‘multipanelfigure’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$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:
there is no package called 'webshot'
Execution halted
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
Packages suggested but not available for checking: ‘dggrids’ ‘INLA’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: ‘RWeka’ ‘FSelector’
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 105-122 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      1.9Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    exdata   5.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.9Mb
    vign       1.4Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R         6.3Mb
    extdata   1.4Mb
Error in re-building vignettes:
  ...
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.1.0
Loading required package: sp
Loading required package: geoR
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2.1 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: raster
Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
Execution halted