Last updated on 2025-03-25 08:59:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.1.2 | 23.73 | 230.50 | 254.23 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.1.2 | 13.16 | 152.14 | 165.30 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.1.2 | 421.96 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 2.1.2 | 374.17 | ERROR | |||
| r-devel-macos-arm64 | 2.1.2 | 85.00 | OK | |||
| r-devel-macos-x86_64 | 2.1.2 | 170.00 | OK | |||
| r-devel-windows-x86_64 | 2.1.2 | 36.00 | 255.00 | 291.00 | OK | |
| r-patched-linux-x86_64 | 2.1.2 | 24.93 | 234.08 | 259.01 | OK | |
| r-release-linux-x86_64 | 2.1.2 | 17.64 | 226.91 | 244.55 | OK | |
| r-release-macos-arm64 | 2.1.2 | 111.00 | OK | |||
| r-release-macos-x86_64 | 2.1.2 | 279.00 | OK | |||
| r-release-windows-x86_64 | 2.1.2 | 31.00 | 253.00 | 284.00 | OK | |
| r-oldrel-macos-arm64 | 2.1.2 | 108.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.1.2 | 251.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.1.2 | 40.00 | 290.00 | 330.00 | OK |
Version: 2.1.2
Check: examples
Result: ERROR
Running examples in ‘rbiom-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: taxa_boxplot
> ### Title: Visualize BIOM data with boxplots.
> ### Aliases: taxa_boxplot
>
> ### ** Examples
>
> library(rbiom)
>
> biom <- rarefy(hmp50)
>
> taxa_boxplot(biom, stat.by = "Body Site", stripe = TRUE)
> taxa_boxplot(biom, layers = "bed", rank = c("Phylum", "Genus"), flip = TRUE)
> taxa_boxplot(
+ biom = subset(biom, `Body Site` %in% c('Saliva', 'Stool')),
+ taxa = 3,
+ layers = "ps",
+ stat.by = "Body Site",
+ colors = c('Saliva' = "blue", 'Stool' = "red") )
Error in attributes(.Data) <- c(attributes(.Data), attrib) :
Cannot modify attributes on primitive functions
Calls: taxa_boxplot ... %>% -> plot_build -> trans_new -> as.cmd -> structure
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
adiv_boxplot 5.097 0.127 5.887
adiv_corrplot 4.278 0.157 5.082
bdiv_heatmap 4.031 0.018 5.128
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.2
Check: tests
Result: ERROR
Running ‘testthat.r’ [22s/26s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
> library(testthat)
> library(rbiom)
>
> test_check("rbiom")
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
══ Skipped tests (33) ══════════════════════════════════════════════════════════
• On CRAN (33): 'test-bdiv_heatmap.r:5:3', 'test-bdiv_ord_plot.r:6:3',
'test-biom_merge.r:11:3', 'test-biom_ply.r:9:3', 'test-biom_ply.r:48:3',
'test-boxplot_build.r:3:3', 'test-cache.r:3:3', 'test-convert.r:5:3',
'test-convert.r:24:3', 'test-convert.r:40:3', 'test-corrplot.r:11:3',
'test-distmat_ord_table.r:6:3', 'test-import_table.r:13:3',
'test-plot_heatmap.r:15:3', 'test-plot_palettes.r:6:3',
'test-provenance.r:3:3', 'test-rarefy.r:3:3', 'test-rbiom-deprecated.r:3:3',
'test-rbiom_objects.r:24:3', 'test-read_biom.r:3:3', 'test-read_fasta.r:3:3',
'test-read_tree.r:7:3', 'test-s3_methods.r:3:3', 'test-stats_emmeans.r:8:3',
'test-stats_wilcox.r:3:3', 'test-taxa_heatmap.r:5:3', 'test-taxa_map.r:3:3',
'test-taxa_stacked.r:5:3', 'test-taxa_table.r:3:3', 'test-utils.r:3:3',
'test-validate.r:3:3', 'test-write_biom.r:15:3', 'test-write_xlsx.r:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-boxplot.r:7:3'): boxplot ───────────────────────────────────────
Error in `attributes(.Data) <- c(attributes(.Data), attrib)`: Cannot modify attributes on primitive functions
Backtrace:
▆
1. ├─testthat::expect_silent(taxa_boxplot(rare5)) at test-boxplot.r:7:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─rbiom::taxa_boxplot(rare5)
10. │ ├─base::with(...)
11. │ └─base::with.default(...)
12. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
13. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
14. │ ├─base::do.call(stats_boxplot, as.list(environment()))
15. │ └─rbiom (local) `<fn>`(...)
16. │ └─rbiom:::boxplot_build(list2env(params))
17. │ └─params %>% plot_facets() %>% boxplot_stats() %>% plot_build()
18. └─rbiom:::plot_build(.)
19. ├─rbiom:::trans_new(...)
20. └─rbiom:::as.cmd(base::sqrt)
21. └─base::structure(eval(expr), display = cmd)
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.1.2
Check: examples
Result: ERROR
Running examples in ‘rbiom-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: taxa_boxplot
> ### Title: Visualize BIOM data with boxplots.
> ### Aliases: taxa_boxplot
>
> ### ** Examples
>
> library(rbiom)
>
> biom <- rarefy(hmp50)
>
> taxa_boxplot(biom, stat.by = "Body Site", stripe = TRUE)
> taxa_boxplot(biom, layers = "bed", rank = c("Phylum", "Genus"), flip = TRUE)
> taxa_boxplot(
+ biom = subset(biom, `Body Site` %in% c('Saliva', 'Stool')),
+ taxa = 3,
+ layers = "ps",
+ stat.by = "Body Site",
+ colors = c('Saliva' = "blue", 'Stool' = "red") )
Error in attributes(.Data) <- c(attributes(.Data), attrib) :
Cannot modify attributes on primitive functions
Calls: taxa_boxplot ... %>% -> plot_build -> trans_new -> as.cmd -> structure
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.2
Check: tests
Result: ERROR
Running ‘testthat.r’ [16s/19s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
> library(testthat)
> library(rbiom)
>
> test_check("rbiom")
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
══ Skipped tests (33) ══════════════════════════════════════════════════════════
• On CRAN (33): 'test-bdiv_heatmap.r:5:3', 'test-bdiv_ord_plot.r:6:3',
'test-biom_merge.r:11:3', 'test-biom_ply.r:9:3', 'test-biom_ply.r:48:3',
'test-boxplot_build.r:3:3', 'test-cache.r:3:3', 'test-convert.r:5:3',
'test-convert.r:24:3', 'test-convert.r:40:3', 'test-corrplot.r:11:3',
'test-distmat_ord_table.r:6:3', 'test-import_table.r:13:3',
'test-plot_heatmap.r:15:3', 'test-plot_palettes.r:6:3',
'test-provenance.r:3:3', 'test-rarefy.r:3:3', 'test-rbiom-deprecated.r:3:3',
'test-rbiom_objects.r:24:3', 'test-read_biom.r:3:3', 'test-read_fasta.r:3:3',
'test-read_tree.r:7:3', 'test-s3_methods.r:3:3', 'test-stats_emmeans.r:8:3',
'test-stats_wilcox.r:3:3', 'test-taxa_heatmap.r:5:3', 'test-taxa_map.r:3:3',
'test-taxa_stacked.r:5:3', 'test-taxa_table.r:3:3', 'test-utils.r:3:3',
'test-validate.r:3:3', 'test-write_biom.r:15:3', 'test-write_xlsx.r:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-boxplot.r:7:3'): boxplot ───────────────────────────────────────
Error in `attributes(.Data) <- c(attributes(.Data), attrib)`: Cannot modify attributes on primitive functions
Backtrace:
▆
1. ├─testthat::expect_silent(taxa_boxplot(rare5)) at test-boxplot.r:7:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─rbiom::taxa_boxplot(rare5)
10. │ ├─base::with(...)
11. │ └─base::with.default(...)
12. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
13. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
14. │ ├─base::do.call(stats_boxplot, as.list(environment()))
15. │ └─rbiom (local) `<fn>`(...)
16. │ └─rbiom:::boxplot_build(list2env(params))
17. │ └─params %>% plot_facets() %>% boxplot_stats() %>% plot_build()
18. └─rbiom:::plot_build(.)
19. ├─rbiom:::trans_new(...)
20. └─rbiom:::as.cmd(base::sqrt)
21. └─base::structure(eval(expr), display = cmd)
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.1.2
Check: examples
Result: ERROR
Running examples in ‘rbiom-Ex.R’ failed
The error most likely occurred in:
> ### Name: taxa_boxplot
> ### Title: Visualize BIOM data with boxplots.
> ### Aliases: taxa_boxplot
>
> ### ** Examples
>
> library(rbiom)
>
> biom <- rarefy(hmp50)
>
> taxa_boxplot(biom, stat.by = "Body Site", stripe = TRUE)
> taxa_boxplot(biom, layers = "bed", rank = c("Phylum", "Genus"), flip = TRUE)
> taxa_boxplot(
+ biom = subset(biom, `Body Site` %in% c('Saliva', 'Stool')),
+ taxa = 3,
+ layers = "ps",
+ stat.by = "Body Site",
+ colors = c('Saliva' = "blue", 'Stool' = "red") )
Error in attributes(.Data) <- c(attributes(.Data), attrib) :
Cannot modify attributes on primitive functions
Calls: taxa_boxplot ... %>% -> plot_build -> trans_new -> as.cmd -> structure
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.1.2
Check: tests
Result: ERROR
Running ‘testthat.r’ [34s/48s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
> library(testthat)
> library(rbiom)
>
> test_check("rbiom")
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
══ Skipped tests (33) ══════════════════════════════════════════════════════════
• On CRAN (33): 'test-bdiv_heatmap.r:5:3', 'test-bdiv_ord_plot.r:6:3',
'test-biom_merge.r:11:3', 'test-biom_ply.r:9:3', 'test-biom_ply.r:48:3',
'test-boxplot_build.r:3:3', 'test-cache.r:3:3', 'test-convert.r:5:3',
'test-convert.r:24:3', 'test-convert.r:40:3', 'test-corrplot.r:11:3',
'test-distmat_ord_table.r:6:3', 'test-import_table.r:13:3',
'test-plot_heatmap.r:15:3', 'test-plot_palettes.r:6:3',
'test-provenance.r:3:3', 'test-rarefy.r:3:3', 'test-rbiom-deprecated.r:3:3',
'test-rbiom_objects.r:24:3', 'test-read_biom.r:3:3', 'test-read_fasta.r:3:3',
'test-read_tree.r:7:3', 'test-s3_methods.r:3:3', 'test-stats_emmeans.r:8:3',
'test-stats_wilcox.r:3:3', 'test-taxa_heatmap.r:5:3', 'test-taxa_map.r:3:3',
'test-taxa_stacked.r:5:3', 'test-taxa_table.r:3:3', 'test-utils.r:3:3',
'test-validate.r:3:3', 'test-write_biom.r:15:3', 'test-write_xlsx.r:3:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-boxplot.r:7:3'): boxplot ───────────────────────────────────────
Error in `attributes(.Data) <- c(attributes(.Data), attrib)`: Cannot modify attributes on primitive functions
Backtrace:
▆
1. ├─testthat::expect_silent(taxa_boxplot(rare5)) at test-boxplot.r:7:3
2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
3. │ ├─testthat (local) .capture(...)
4. │ │ ├─withr::with_output_sink(...)
5. │ │ │ └─base::force(code)
6. │ │ ├─base::withCallingHandlers(...)
7. │ │ └─base::withVisible(code)
8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
9. ├─rbiom::taxa_boxplot(rare5)
10. │ ├─base::with(...)
11. │ └─base::with.default(...)
12. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
13. │ └─base::eval(substitute(expr), data, enclos = parent.frame())
14. │ ├─base::do.call(stats_boxplot, as.list(environment()))
15. │ └─rbiom (local) `<fn>`(...)
16. │ └─rbiom:::boxplot_build(list2env(params))
17. │ └─params %>% plot_facets() %>% boxplot_stats() %>% plot_build()
18. └─rbiom:::plot_build(.)
19. ├─rbiom:::trans_new(...)
20. └─rbiom:::as.cmd(base::sqrt)
21. └─base::structure(eval(expr), display = cmd)
[ FAIL 1 | WARN 0 | SKIP 33 | PASS 190 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc