Last updated on 2026-10-21 05:56:39 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 7.1.5 | 20.60 | 167.65 | 188.25 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 7.1.5 | 12.75 | 101.14 | 113.89 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 7.1.5 | 13.00 | 110.11 | 123.11 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 7.1.5 | 13.00 | 113.72 | 126.72 | OK | |
| r-devel-windows-x86_64 | 7.1.5 | 23.00 | 267.00 | 290.00 | OK | |
| r-patched-linux-x86_64 | 7.1.5 | 21.46 | 154.87 | 176.33 | OK | |
| r-release-linux-x86_64 | 7.1.5 | 17.55 | 154.59 | 172.14 | OK | |
| r-release-macos-arm64 | 7.1.5 | 5.00 | 47.00 | 52.00 | OK | |
| r-release-macos-x86_64 | 7.1.5 | 14.00 | 244.00 | 258.00 | OK | |
| r-release-windows-x86_64 | 7.1.5 | 24.00 | 197.00 | 221.00 | OK | |
| r-oldrel-macos-arm64 | 7.1.5 | 5.00 | 50.00 | 55.00 | OK | |
| r-oldrel-macos-x86_64 | 7.1.5 | 13.00 | 228.00 | 241.00 | OK | |
| r-oldrel-windows-x86_64 | 7.1.5 | 30.00 | 234.00 | 264.00 | OK |
Version: 7.1.5
Check: Rd contents
Result: NOTE
Rd files without \usage:
‘panel.BL.bwplot.Rd’
\arguments should not be documented without \usage.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 7.1.5
Check: examples
Result: ERROR
Running examples in ‘BoutrosLab.plotting.general-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create.multiplot
> ### Title: Joins plots together
> ### Aliases: create.multiplot
> ### Keywords: hplot
>
> ### ** Examples
>
> set.seed(12345);
>
> # begin by creating the individual plots which will be combined into a multiplot
> dist <- data.frame(
+ a = rnorm(100, 1),
+ b = rnorm(100, 3),
+ c = rnorm(100, 5)
+ );
>
> simple.data <- data.frame(
+ x = c(dist$a, dist$b, dist$c),
+ y = rep(LETTERS[1:3], each = 100)
+ );
>
> fill.squares <- matrix(c(1, 0, 0, 0, 1, 0, 0, 0, 1), ncol = 3, byrow = TRUE);
> rownames(fill.squares) <- c("Drug I only", "Drug II only" , "Drugs I & II");
> colnames(fill.squares) <- levels(factor(simple.data$y));
>
> # Create plot # 1
> simple.boxplot <- create.boxplot(
+ formula = x ~ y,
+ data = simple.data,
+ col = 'lightgrey'
+ );
>
> # Create plot # 2
> simple.heatmap <- create.heatmap(
+ x = t(fill.squares),
+ clustering.method = 'none',
+ shrink = 0.8,
+ colour.scheme = c("white", "grey20"),
+ fill.colour = "white",
+ print.colour.key = FALSE
+ );
>
> # Simple example of multiplot
> # This example uses the defaults set in simple.heatmap and simple.boxplot
> create.multiplot(
+ # filename = tempfile(pattern = 'Multiplot_Simple', fileext = '.tiff'),
+ plot.objects = list(simple.heatmap, simple.boxplot),
+ main = "Simple",
+ xlab.label = c("Patient Group"),
+ # The plotting function throws an error if this is not included
+ ylab.label = c("Sugar Level", "Drug Regimen"),
+ ylab.padding = 7,
+ # Parameters set in the multiplot will override settings in individual plots
+ xaxis.cex = 0.7,
+ yaxis.cex = 0.7,
+ resolution = 100
+ );
Warning in class(limits) <- if (all(class.lim[[1]] == "integer")) "numeric" else class.lim[[1]] :
NAs introduced by coercion
>
> # Simple example of multiplot with adjusted plot sizes
> create.multiplot(
+ # filename = tempfile(pattern = 'Multiplot_Simple_Plot_Sizes', fileext = '.tiff'),
+ plot.objects = list(simple.heatmap, simple.boxplot),
+ main = "Simple plot sizes",
+ xlab.label = c("Patient Group"),
+ # y-axis labels must be spaced with tabs or spaces to properly align
+ ylab.label = c("", "Sugar Level", "", "Drug Regimen"),
+ ylab.padding = 7,
+ xaxis.cex = 0.7,
+ yaxis.cex = 0.7,
+ # Set the relative heights of the plots
+ panel.heights = c(3,1),
+ resolution = 100
+ );
Warning in class(limits) <- if (all(class.lim[[1]] == "integer")) "numeric" else class.lim[[1]] :
NAs introduced by coercion
>
> simple.violin <- create.violinplot(
+ formula = x ~ y,
+ data = simple.data,
+ col = 'lightgrey'
+ );
>
> # Simple example of multiplot with custom layout
> create.multiplot(
+ # filename = tempfile(pattern = 'Multiplot_Simple_Layout', fileext = '.tiff'),
+ plot.objects = list(simple.heatmap, simple.boxplot, simple.violin),
+ main = "Simple layout",
+ xlab.label = c("Patient Group"),
+ ylab.label = c("", "Sugar Level", "", "Drug Regimen"),
+ ylab.padding = 7,
+ xaxis.cex = 0.7,
+ yaxis.cex = 0.7,
+ panel.heights = c(3,1),
+ # Set how many rows & columns are in the layout
+ plot.layout = c(2,2),
+ # Set whether to plot or not in the space (fills from bottom left to top right)
+ layout.skip = c(FALSE, TRUE, FALSE, FALSE),
+ # Move plots closer together
+ x.spacing = 0,
+ # Remove doubled internal axis
+ yat = list(
+ seq(1,3,1),
+ seq(-2, 8, 2),
+ c()
+ ),
+ resolution = 100
+ );
Warning in class(limits) <- if (all(class.lim[[1]] == "integer")) "numeric" else class.lim[[1]] :
NAs introduced by coercion
>
> # Example of how to take parameter values from individual plots
> # This programming structure allows for including the individual customization
> # of plots to the final multiplot
> all_data <- data.frame(
+ a = rnorm(n = 25, mean = 0, sd = 0.75),
+ b = rnorm(n = 25, mean = 0, sd = 0.75),
+ c = rnorm(n = 25, mean = 0, sd = 0.75),
+ d = rnorm(n = 25, mean = 0, sd = 0.75),
+ e = rnorm(n = 25, mean = 0, sd = 0.75),
+ f = rnorm(n = 25, mean = 0, sd = 0.75),
+ x = rnorm(n = 25, mean = 5),
+ y = seq(1, 25, 1)
+ );
>
> plot.heatmap <- function(all_data){
+ # save the parameter values that will be reused in the multiplot
+ multiplot_visuals <- list(
+ xlab.label = '',
+ xaxis.labels = NULL,
+ xat = NULL,
+ ylab.label = 'Genes of Interest',
+ yaxis.labels = c("BRCA1", "BRCA2", "APC", "TIN", "ARG", "FOO"),
+ yat = c(1,2,3,4,5,6)
+ );
+
+ # create the plot -- this allows for previewing of the individual plot
+ heatmap.formatted <- create.heatmap(
+ x = all_data[,1:6],
+ clustering.method = 'none',
+ colour.scheme = c('magenta','white','green'),
+ print.colour.key = FALSE,
+ xlab.label = multiplot_visuals$xlab.label,
+ xaxis.lab = multiplot_visuals$xaxis.labels,
+ xat = multiplot_visuals$xat,
+ ylab.label = multiplot_visuals$ylab.label,
+ yaxis.lab = multiplot_visuals$yaxis.labels,
+ yat = multiplot_visuals$yat
+ );
+
+ # return both the plot and the relevant parameter values
+ return(
+ list(
+ the_plot = heatmap.formatted,
+ visuals = multiplot_visuals
+ )
+ )
+ }
>
> plot.barplot <- function(all_data) {
+
+ # save the parameter values that will be reused in the multiplot
+ multiplot_visuals <- list(
+ xlab.label = '',
+ xaxis.labels = NULL,
+ xat = NULL,
+ ylab.label = 'Importance',
+ yaxis.labels = seq(1, ceiling(max(all_data$x)), 1),
+ yat = seq(1, ceiling(max(all_data$x)), 1)
+ );
+
+ # create the plot -- this allows for previewing of the individual plot
+ barplot.formatted <- create.barplot(
+ formula = x ~ y,
+ data = all_data[,7:8],
+ border.lwd = 0,
+ col = 'grey',
+ xlab.label = multiplot_visuals$xlab.label,
+ xaxis.lab = multiplot_visuals$xaxis.labels,
+ xat = multiplot_visuals$xat,
+ ylab.label = multiplot_visuals$ylab.label,
+ yaxis.lab = multiplot_visuals$yaxis.labels,
+ yat = multiplot_visuals$yat
+ );
+
+ # return both the plot and the relevant parameter values
+ return(
+ list(
+ the_plot = barplot.formatted,
+ visuals = multiplot_visuals
+ )
+ )
+ }
>
> plot_functions <- c('plot.heatmap', 'plot.barplot');
>
> # run the functions
> all_plots <- lapply(
+ plot_functions,
+ function(funName){
+ eval(parse(text = paste0(funName, '(all_data)')))
+ }
+ );
>
> create.multiplot(
+ # filename = tempfile(pattern = 'Multiplot_Formatting', fileext = '.tiff'),
+ main = "Formatting",
+ plot.objects = lapply(all_plots, function(aPlot) aPlot$the_plot),
+ panel.heights = c(1,3),
+ xaxis.cex = 1,
+ yaxis.cex = 1,
+ ylab.padding = 8,
+ yat = lapply(all_plots,function(aPlot) aPlot$visuals$yat),
+ xlab.label = lapply(all_plots,function(aPlot) aPlot$visuals$xlab.label),
+ ylab.label = rev(lapply(all_plots,function(aPlot) aPlot$visuals$ylab.label)),
+ yaxis.labels = lapply(all_plots,function(aPlot) aPlot$visuals$yaxis.labels),
+ resolution = 100
+ );
>
> data_bars <- data.frame(
+ x = sample(x = 5:35, size = 10),
+ y = seq(1,10,1)
+ );
>
> data_cov <- data.frame(
+ x = rnorm(n = 10, mean = 0, sd = 0.75),
+ y = rnorm(n = 10, mean = 0, sd = 0.75),
+ z = rnorm(n = 10, mean = 0, sd = 0.75)
+ );
>
> # Create main barplot
> bars <- create.barplot(
+ formula = x~y,
+ data = data_bars,
+ ylimits = c(0,35),
+ sample.order = 'increasing',
+ border.lwd = 0
+ );
>
> # Make covariate bars out of heatmaps
> cov_1 <- create.heatmap(
+ x = as.matrix(data_bars$y),
+ clustering.method = 'none',
+ scale.data = FALSE,
+ colour.scheme = default.colours(4),
+ grid.col = TRUE,
+ col.colour = 'black',
+ # col.lwd = 10,
+ total.col = 5,
+ print.colour.key = FALSE,
+ yaxis.tck = 0,
+ axes.lwd = 0
+ );
>
> cov_2 <- create.heatmap(
+ x = as.matrix(data_cov$y),
+ clustering.method = 'none',
+ scale.data = FALSE,
+ colour.scheme = c("lightblue","dodgerblue2", "dodgerblue4"),
+ grid.col = TRUE,
+ col.colour = 'black',
+ # col.lwd = 10,
+ total.col = 4,
+ print.colour.key = FALSE,
+ yaxis.tck = 0
+ );
Warning in create.heatmap(x = as.matrix(data_cov$y), clustering.method = "none", :
Colour allocation scheme failed, moving to a default method
>
> cov_3 <- create.heatmap(
+ x = as.matrix(data_cov$z),
+ clustering.method = 'none',
+ scale.data = FALSE,
+ colour.scheme = c("grey","coral1"),
+ grid.col = TRUE,
+ col.colour = 'black',
+ # col.lwd = 10,
+ total.col = 3,
+ print.colour.key = FALSE,
+ yaxis.tck = 0
+ );
>
> # Generate legends outside of individual functions
> legend <- legend.grob(
+ list(
+ legend = list(
+ colours = default.colours(4),
+ title = "Batch",
+ labels = LETTERS[1:4],
+ size = 3,
+ title.cex = 1,
+ label.cex = 1,
+ border = 'black'
+ ),
+ legend = list(
+ colours = c("lightblue","dodgerblue2","dodgerblue4"),
+ title = "Grade",
+ labels = c("Low","Normal","High"),
+ size = 3,
+ title.cex = 1,
+ label.cex = 1,
+ border = 'black'
+ ),
+ legend = list(
+ colours = c("grey","coral1"),
+ title = "Biomarker",
+ labels = c("Not present","Present"),
+ size = 3,
+ title.cex = 1,
+ label.cex = 1,
+ border = 'black'
+ )
+ ),
+ title.just = 'left'
+ );
Error: index out of bounds ("unit" subsetting)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 7.1.5
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘PlottingGuide.Rnw’ using knitr_notangle
Warning in remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 2303, 2363; you may need Sweave2knitr("PlottingGuide.Rnw") to convert it to knitr
Quitting from PlottingGuide.Rnw:1756-1792 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! index out of bounds ("unit" subsetting)
---
Backtrace:
x
1. \-BoutrosLab.plotting.general::legend.grob(...)
2. \-grid::packGrob(...)
3. \-grid:::mod.dims(...)
4. +-grid::unit.c(...)
5. +-dims[(index + 1):(nindex - 1)]
6. \-grid:::`[.unit`(dims, (index + 1):(nindex - 1))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'PlottingGuide.Rnw' failed with diagnostics:
index out of bounds ("unit" subsetting)
--- failed re-building ‘PlottingGuide.Rnw’
SUMMARY: processing the following file failed:
‘PlottingGuide.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc