- using R Under development (unstable) (2025-10-27 r88972)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 21.1.4
flang version 21.1.4
- running under: Fedora Linux 42 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- checking for file ‘lolliplot/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘lolliplot’ version ‘0.2.2’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... OK
- 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 ‘lolliplot’ can be installed ... [29s/125s] 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [8s/43s] OK
- checking whether the package can be loaded with stated dependencies ... [7s/24s] OK
- checking whether the package can be unloaded cleanly ... [7s/22s] OK
- checking whether the namespace can be loaded with stated dependencies ... [7s/24s] OK
- checking whether the namespace can be unloaded cleanly ... [8s/39s] OK
- checking loading without being on the library search path ... [8s/35s] OK
- checking use of S3 registration ... 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 ... [45s/171s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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 examples ... [9s/38s] ERROR
Running examples in ‘lolliplot-Ex.R’ failed
The error most likely occurred in:
> ### Name: lolliplot
> ### Title: Lolliplots
> ### Aliases: lolliplot
>
> ### ** Examples
>
> SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402)
> x <- sample.int(100, length(SNP))
> SNP.gr <- GenomicRanges::GRanges("chr1", IRanges::IRanges(SNP, width=1, names=paste0("snp", SNP)),
+ value1=x, value2=100-x)
> SNP.gr$color <- rep(list(c("red", 'blue')), length(SNP))
> SNP.gr$border <- sample.int(7, length(SNP), replace=TRUE)
> features <- GenomicRanges::GRanges(
+ "chr1", IRanges::IRanges(
+ c(1, 501, 1001),
+ width=c(120, 500, 405),
+ names=paste0("block", 1:3)),
+ color="black",
+ fill=c("#FF8833", "#51C6E6", "#DFA32D"),
+ height=c(0.1, 0.05, 0.08),
+ label.parameter.rot=45)
> lolliplot(SNP.gr, features, type="pie")
Error in S4Vectors:::load_package_gracefully("XVector", "by the range() method ", :
Could not load package XVector. Is it installed?
Note that the XVector package is required by the range() method for
CompressedIRangesList objects. Please install it with:
BiocManager::install("XVector")
Calls: lolliplot ... .local -> .range_CompressedIRangesList -> <Anonymous>
Execution halted
- checking PDF version of manual ... [7s/25s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 1 ERROR