Running 'test_plotting_functions.R' [174s]
  Running 'testthat.R' [163s]
Running the tests in 'tests/test_plotting_functions.R' failed.
Complete output:
  > ### TEST-SUITE #####################################################################################
  > # Description: This script runs the plotting code in BoutrosLab.plotting.general for testing purposes
  > # The plots are stored in variables and plotted together in a single multiple in order to save plot-generation time
  > 
  > warning(paste(
  +     'BPG will discontinue this test file in v8.0.0.',
  +     'Instead, tests will use the standard testthat format.',
  +     'For more information, see https://testthat.r-lib.org/'
  +     ));
  Warning message:
  BPG will discontinue this test file in v8.0.0. Instead, tests will use the standard testthat format. For more information, see https://testthat.r-lib.org/ 
  > 
  > ### LOAD LIBRARY ###################################################################################
  > library(BoutrosLab.plotting.general);
  Loading required package: lattice
  Loading required package: latticeExtra
  Loading required package: cluster
  Loading required package: hexbin
  Loading required package: grid
  
  Attaching package: 'BoutrosLab.plotting.general'
  
  The following object is masked from 'package:stats':
  
      dist
  
  > 
  > ### PLOTTING FUNCTIONS #############################################################################
  > test.data <- data.frame(
  + 	x = 1:10,
  + 	y = LETTERS[1:10],
  + 	z = rnorm(10),
  + 	type = rep(LETTERS[1:2], 5),
  + 	stringsAsFactors = TRUE
  + 	);
  > 
  > # testing legend.grob
  > covariate.legend <- list(
  + 	legend = list(
  + 		colours = default.colours(2),
  + 		labels = levels(test.data$type)[1:2]
  + 		)
  + 	);
  > 
  > legend.grob2 <- legend.grob(
  + 	legends = covariate.legend
  + 	);
  Warning message:
  In FUN(X[[i]], ...) : 'x' is NULL so the result will be NULL
  > 
  > # testing covariates.grob
  > covariate.colours1 <- as.character(test.data$type);
  > covariate.colours1[covariate.colours1 == 'A'] <- default.colours(2)[1];
  > covariate.colours1[covariate.colours1 == 'B'] <- default.colours(2)[2];
  > 
  > # create an object to draw the covariates from
  > covariates1 <- list(
  + 	rect = list(
  + 		col = 'black',
  + 		fill = covariate.colours1,
  + 		lwd = 1.5
  + 		)
  + 	);
  > 
  > covariates.grob1 <- covariates.grob(
  + 	covariates = covariates1,
  + 	ord = c(1:10),
  + 	side = 'top',
  + 	size = .8
  + 	);
  > 
  > barplot <- create.barplot(
  + 	formula = y ~ x,
  + 	data = test.data,
  + 	legend = list(
  + 		bottom = list(
  + 			fun = covariates.grob1
  + 			),
  + 		right = list(
  + 			fun = legend.grob2
  + 			),
  + 		inside = list(
  + 			fun = draw.key,
  + 			args = list(
  + 				key = get.corr.key(
  + 					x = test.data$x,
  + 					y = test.data$y,
  + 					label.items = c('spearman', 'spearman.p', 'kendall', 'beta1')
  + 					)
  + 				),
  + 			x = 0.5,
  + 			y = 0.5
  + 			)
  + 		),
  + 	description = 'testing metadata'
  + 	);
  Warning messages:
  1: In model.response(mf, "numeric") :
    using type = "numeric" with a factor response will be ignored
  2: In Ops.factor(y, z$residuals) : '-' not meaningful for factors
  > 
  > # this isn't printed anywhere
  > dend <- create.dendrogram(
  + 	x = data.frame(test.data$z, rnorm(10))
  + 	);
  > 
  > # # This is the slowest running function
  > # heatmap <- create.heatmap(
  > # 	x = as.matrix(test.data$z),
  > # 	clustering.method = 'none'
  > # 	);
  > 
  > dotmap <- create.dotmap(
  + 	x = test.data$z
  + 	);
  > 
  > hexbin <- create.hexbinplot(	
  + 	formula = z ~ x,
  + 	data = test.data
  + 	);
  > 
  > # Also using generate.at.final()
  > density <- create.densityplot(
  + 	x = list(
  + 		a = test.data$x, 
  + 		b = test.data$z
  + 		),
  + 	xat = c(0, 1.1, 1.5, 1, 6, 4),
  + 	yat = c(0.34, 0.38, 0.7),
  + 	type = c('g', 'l'),
  + 	resolution = 100
  + 	);
  > 
  > manhattanplot <- create.manhattanplot(
  + 	formula = x ~ y,
  + 	data = test.data
  + 	);
  > 
  > polygonplot <- create.polygonplot(	
  + 	formula = NA ~ x,
  + 	data = test.data,
  + 	max = test.data$x,
  + 	min = test.data$z,
  + 	xlimits = c(0, 10),
  + 	ylimits = c(-2, 10)
  + 	);
  > 
  > qqcomp <- create.qqplot.comparison(
  + 	x = list(test.data$x, test.data$z)
  + 	);
  > 
  > scatter <- create.scatterplot(
  + 	formula = x ~ z,
  + 	data = test.data
  + 	);
  > 
  > seg <- create.segplot(
  + 	formula = y ~ x + z,
  + 	data = test.data
  + 	);
  > 
  > violin <- create.violinplot(
  + 	formula = y ~ z,
  + 	data = test.data
  + 	);
  > 
  > strip <- create.stripplot(
  + 	formula = z ~ y,
  + 	data = test.data
  + 	);
  > 
  > boxplot <- create.boxplot(
  + 	formula = x ~ y,
  + 	data = test.data
  + 	);
  > 
  > # these do not easily join the multiplot
  > histogram <- create.histogram(
  + 	x = test.data$z
  + 	);
  > 
  > qqfit <- create.qqplot.fit(
  + 	x = test.data$z
  + 	);
  > 
  > # Plot everything in one plot for quicker running time
  > create.multiplot(
  + 	file = NULL,
  + 	plot.objects = list(polygonplot, manhattanplot, hexbin, dotmap, density, qqcomp, scatter, seg, violin, barplot, strip, boxplot)
  + 	);
  > 
  > ### HELPER FUNCTIONS ###############################################################################
  > 
  > get.line.breaks(1:10);
  [1] 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5 9.5
  > 
  > scientific.notation(1234, 2, type = 'list');
  $base
  [1] "1.23"
  
  $exponent
  [1] 3
  
  > scientific.notation(0, 2);
  [1] 0
  > scientific.notation(c(1234, 1234), 1);
  expression("1.2" %*% 10^3, "1.2" %*% 10^3)
  > 
  > # This returns the same thing as when type = 'expression' - should something be changed?
  > scientific.notation(c(1234, 1234), 1, type = 'list');
  expression("1.2" %*% 10^3, "1.2" %*% 10^3)
  > 
  > display.statistical.result(1234);
  expression("P: 1200")
  > 
  > ### COLOUR FUNCTIONS ###############################################################################
  > default.colours(12, is.greyscale = FALSE);
   [1] "orange"      "chartreuse4" "darkorchid4" "gold"        "dodgerblue" 
   [6] "firebrick3"  "yellowgreen" "darkorange1" "slateblue4"  "seagreen3"  
  [11] "violetred3"  "turquoise3" 
  > default.colours(5, palette.type = 'chromosomes', is.greyscale = FALSE);
  [1] "darkred"     "firebrick1"  "pink1"       "darkorange3" "darkorange" 
  > default.colours(5, palette.type = 'seq');
  [1] "#C1D8AA" "#83B155" "#458B00" "#2E5C00" "#172E00"
  > default.colours(c(4, 4), palette.type = c('seq', 'div'));
  [[1]]
  [1] "#C1D8AA" "#83B155" "#458B00" "#2E5C00"
  
  [[2]]
  [1] "#B32B2B" "#DD4E4E" "#EB7C7C" "#F7BEBE"
  
  > 
  > # display.colours(default.colours(3));
  > # display.colours(grey(0.5));
  > 
  > force.colour.scheme(c('stopgain snv', 'splicing'), 'annovar.annotation');
  [1] "orchid4" "gold1"  
  > 
  > proc.time()
     user  system elapsed 
     1.45    0.14    1.57 
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(BoutrosLab.plotting.general)
  Loading required package: lattice
  Loading required package: latticeExtra
  Loading required package: cluster
  Loading required package: hexbin
  Loading required package: grid
  
  Attaching package: 'BoutrosLab.plotting.general'
  
  The following object is masked from 'package:stats':
  
      dist
  
  > 
  > test_check('BoutrosLab.plotting.general')
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 18 ]
  
  [ FAIL 0 | WARN 3 | SKIP 0 | PASS 18 ]
  > 
  > proc.time()
     user  system elapsed 
     1.68    0.34    2.00