- using R version 4.3.3 (2024-02-29)
- using platform: aarch64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.4
- using session charset: UTF-8
- checking for file ‘geneviewer/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘geneviewer’ version ‘0.1.10’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘pwalign’
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘geneviewer’ can be installed ... [3s/4s] OK
See the install log for details.
- checking installed package size ... OK
- checking package directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [0s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
- checking loading without being on the library search path ... [0s/1s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [3s/3s] OK
- checking Rd files ... [0s/0s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking examples ... [2s/3s] ERROR
Running examples in ‘geneviewer-Ex.R’ failed
The error most likely occurred in:
> ### Name: GC_links
> ### Title: Add Links to GC Chart
> ### Aliases: GC_links
>
> ### ** Examples
>
> # Add links between all groups in each cluster
> genes_data <- data.frame(
+ start = c(10, 90, 130, 170, 240, 250, 300, 340, 380, 420),
+ end = c(40, 120, 160, 200, 210, 270, 330, 370, 410, 450),
+ name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5',
+ 'Gene 6', 'Gene 7', 'Gene 8', 'Gene 9', 'Gene 10'),
+ group = c('A', 'B', 'C', 'A', 'B', 'C', 'A', 'B', 'C', 'D'),
+ identity = c(NA, NA, NA, 50, 40, 100, 60, 65, 20, NA),
+ similarity = c(NA, NA, NA, 40, 30, 90, 50, 55, 10, NA),
+ cluster = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3)
+ )
> GC_chart(genes_data,
+ cluster = "cluster",
+ height = "200px") %>%
+ GC_links(
+ group = "group",
+ value1 = "A",
+ value2 = "B",
+ measure = "identity",
+ label = FALSE) %>%
+ GC_labels(label = "group")
>
> # Add links between group A of cluster 1 and A and B of cluster 2
> GC_chart(genes_data,
+ cluster = "cluster",
+ height = "200px") %>%
+ GC_labels(label = "group") %>%
+ GC_links(group = "group",
+ value1 = c("A", "A"),
+ value2 = c("B", "A"),
+ label = FALSE,
+ cluster = c(1,2))
>
> # Style links and color bar
> GC_chart(genes_data,
+ cluster = "cluster",
+ height = "200px"
+ ) %>%
+ GC_links(
+ group = "group",
+ data = NULL,
+ curve = TRUE,
+ measure = "identity",
+ show_links = TRUE,
+ label = TRUE,
+ normal_color = "#1f77b4",
+ inverted_color = "#d62728",
+ use_group_colors = FALSE,
+ color_bar = TRUE,
+ colorBarOptions = list(
+ x = 0,
+ y = 24,
+ width = 10,
+ height = 60,
+ labelOptions = list(
+ fontSize = 8,
+ xOffset = 2,
+ yOffset = 0
+ # Any other CSS style
+ ),
+ titleOptions = list(
+ fontSize = 10,
+ xOffset = 2,
+ yOffset = 0
+ # Any other CSS style
+ ),
+ barOptions = list(
+ stroke = "#000",
+ strokeWidth = 0.5,
+ opacity = 1
+ # Any other CSS style
+ )
+ ),
+ linkWidth = 1,
+ linkStyle = list(
+ stroke = "black",
+ strokeWidth = 0.5,
+ fillOpacity = 0.4
+ # Any other CSS style
+ ),
+ labelStyle = list(
+ fontSize = "8px"
+ # Any other CSS style
+ )
+ ) %>%
+ GC_labels(label = "group", cluster = 1) %>%
+ GC_clusterLabel()
Warning in file.copy(from, to, overwrite = TRUE, recursive = isdir, copy.mode = FALSE) :
problem creating directory /Volumes/Builds/packages/big-sur-arm64/results/4.3/geneviewer.Rcheck/geneviewer/htmlwidgets/lib/FileSaver-2.0.4: No space left on device
Warning in file.copy(from, to, overwrite = TRUE, recursive = isdir, copy.mode = FALSE) :
problem creating directory /Volumes/Builds/packages/big-sur-arm64/results/4.3/geneviewer.Rcheck/geneviewer/htmlwidgets/lib/html2canvas-1.4.1: No space left on device
Warning in dir.create(target_dir) :
cannot create dir 'lib/geneviewer-0.1.10', reason 'No space left on device'
Error in normalizePath(target_dir, "/", TRUE) :
path[1]="lib/geneviewer-0.1.10": No such file or directory
Calls: <Anonymous> ... lapply -> FUN -> copyDependencyToDir -> normalizePath
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [4s/4s] OK
Running ‘testthat.R’ [4s/4s]
- checking PDF version of manual ... [4s/4s] OK
- DONE
Status: 1 ERROR, 1 NOTE
- using check arguments '--no-clean-on-error '