- using R Under development (unstable) (2025-06-11 r88304 ucrt)
- using platform: x86_64-w64-mingw32
- R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
- running under: Windows Server 2022 x64 (build 20348)
- using session charset: UTF-8
- checking for file 'MetaComp/DESCRIPTION' ... OK
- this is package 'MetaComp' version '1.1.2'
- 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 hidden files and directories ... OK
- checking for portable file names ... OK
- checking whether package 'MetaComp' can be installed ... 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 ... [1s] OK
- checking whether the package can be loaded with stated dependencies ... [1s] OK
- checking whether the package can be unloaded cleanly ... [1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s] OK
- checking whether the namespace can be unloaded cleanly ... [1s] OK
- checking loading without being on the library search path ... [1s] 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 ... [4s] OK
- checking Rd files ... [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 LazyData ... INFO
'LazyData' is specified without a 'data' directory
- checking examples ... [2s] ERROR
Running examples in 'MetaComp-Ex.R' failed
The error most likely occurred in:
> ### 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 Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg, :
Graphics API version mismatch
Calls: plot_edge_assignment -> <Anonymous> -> Cairo
Execution halted
- checking for unstated dependencies in 'tests' ... OK
- checking tests ... [6s] ERROR
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(MetaComp)
>
> test_check("MetaComp")
[1] "gottcha"
[1] "kraken"
[ FAIL 14 | WARN 7 | SKIP 0 | PASS 114 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_pipeline.R:28:1'): (code run outside of `test_that()`) ─────────
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_pipeline.R:28:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_bwa_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_bwa_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_diamond_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_diamond_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_gottcha_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_gottcha_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_kraken_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_kraken_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_b.R:73:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_b.R:73:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_d.R:73:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_d.R:73:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_g.R:71:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_g.R:71:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_g2.R:71:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_g2.R:71:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_k.R:73:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_k.R:73:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_m.R:73:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_m.R:73:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_merged_assignment_p.R:74:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_merged_assignment(...) at test_plot_merged_assignment_p.R:74:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_metaphlan_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_metaphlan_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
── Error ('test_plot_pangia_assignment.R:18:1'): (code run outside of `test_that()`) ──
Error in `Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,
units = "in", title = title, ...)`: Graphics API version mismatch
Backtrace:
▆
1. └─MetaComp::plot_edge_assignment(...) at test_plot_pangia_assignment.R:18:1
2. └─Cairo::CairoPDF(...)
3. └─Cairo::Cairo(...)
[ FAIL 14 | WARN 7 | SKIP 0 | PASS 114 ]
Error: Test failures
Execution halted
- checking PDF version of manual ... [19s] OK
- checking HTML version of manual ... [1s] OK
- DONE
Status: 2 ERRORs