Last updated on 2025-12-24 15:52:02 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.2.0 | 28.47 | 499.72 | 528.19 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.2.0 | 19.96 | 330.75 | 350.71 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.2.0 | 52.00 | 805.29 | 857.29 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 1.2.0 | 44.00 | 808.78 | 852.78 | ERROR | |
| r-devel-windows-x86_64 | 1.2.0 | 32.00 | 444.00 | 476.00 | OK | |
| r-patched-linux-x86_64 | 1.2.0 | 34.04 | 459.30 | 493.34 | OK | |
| r-release-linux-x86_64 | 1.2.0 | 25.73 | 462.53 | 488.26 | OK | |
| r-release-macos-arm64 | 1.2.0 | OK | ||||
| r-release-macos-x86_64 | 1.2.0 | 18.00 | 303.00 | 321.00 | OK | |
| r-release-windows-x86_64 | 1.2.0 | 34.00 | 441.00 | 475.00 | OK | |
| r-oldrel-macos-arm64 | 1.2.0 | NOTE | ||||
| r-oldrel-macos-x86_64 | 1.2.0 | 20.00 | 253.00 | 273.00 | NOTE | |
| r-oldrel-windows-x86_64 | 1.2.0 | 42.00 | 592.00 | 634.00 | OK |
Version: 1.2.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [8m/25m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(ggalign)
Loading required package: ggplot2
========================================
ggalign version 1.2.0
If you use it in published research, please cite:
Peng, Y.; Jiang, S.; Song, Y.; et al. ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity. Advanced Science. 2025. doi:10.1002/advs.202507799
========================================
>
> test_check("ggalign")
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`geom_subrect()` subdivide tile into a maximal of 5 rectangles
`geom_subrect()` subdivide tile into a maximal of 9 rectangles
`geom_subrect()` subdivide tile into a maximal of 4 rectangles
`geom_subrect()` subdivide tile into a maximal of 4 rectangles
`geom_subrect()` subdivide tile into a maximal of 4 rectangles
`geom_subtile()` subdivide tile into a maximal of 5 rectangles
`geom_subtile()` subdivide tile into a maximal of 9 rectangles
`geom_subtile()` subdivide tile into a maximal of 4 rectangles
`geom_subtile()` subdivide tile into a maximal of 4 rectangles
`geom_subtile()` subdivide tile into a maximal of 4 rectangles
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NULL
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> heatmap built with `geom_tile()`
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> heatmap built with `geom_tile()`
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> heatmap built with `geom_tile()`
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[ FAIL 2 | WARN 0 | SKIP 89 | PASS 340 ]
══ Skipped tests (89) ══════════════════════════════════════════════════════════
• On CRAN (86): 'test-active.R:11:1', 'test-active.R:45:1',
'test-align-hclust.R:5:1', 'test-align-hclust.R:14:1',
'test-align-hclust.R:23:1', 'test-align-hclust.R:29:1',
'test-align-hclust.R:35:1', 'test-align-hclust.R:41:1',
'test-align-hclust.R:51:1', 'test-align-phylo.R:9:1',
'test-align-phylo.R:36:1', 'test-align-phylo.R:45:1',
'test-align-phylo.R:54:1', 'test-align-phylo.R:63:1',
'test-align-phylo.R:72:1', 'test-alignpatch.R:13:1',
'test-alignpatch.R:27:1', 'test-alignpatch.R:122:1',
'test-alignpatch.R:145:1', 'test-alignpatch.R:205:1',
'test-alignpatch.R:254:1', 'test-alignpatch.R:312:1',
'test-alignpatch.R:354:1', 'test-alignpatch.R:408:1',
'test-alignpatch.R:454:1', 'test-alignpatch.R:523:1', 'test-area.R:17:1',
'test-as-grob.R:1:1', 'test-fortify-matrix.R:18:1',
'test-fortify-matrix.R:76:1', 'test-free-guide.R:49:1', 'test-ggplot.R:1:1',
'test-ggplot.R:20:1', 'test-ggplot.R:59:1', 'test-ggplot.R:87:1',
'test-ggplot.R:105:1', 'test-ggplot.R:123:1', 'test-ggplot.R:141:1',
'test-ggplot.R:210:1', 'test-ggplot.R:231:1', 'test-ggplot.R:240:1',
'test-ggplot.R:261:1', 'test-ggplot.R:276:1', 'test-grid.R:1:1',
'test-grid.R:19:1', 'test-grid.R:50:1', 'test-inset.R:26:1',
'test-inset.R:36:1', 'test-layout-chain.R:13:1', 'test-layout-chain.R:68:1',
'test-layout-chain.R:229:1', 'test-layout-circle.R:35:1',
'test-layout-circle.R:67:1', 'test-layout-heatmap.R:1:1',
'test-layout-heatmap.R:27:1', 'test-layout-heatmap.R:60:1',
'test-layout-heatmap.R:168:1', 'test-layout-heatmap.R:246:1',
'test-layout-heatmap.R:323:1', 'test-layout-quad.R:1:1',
'test-layout-quad.R:9:1', 'test-layout-quad.R:55:1',
'test-layout-quad.R:98:1', 'test-layout-quad.R:129:1',
'test-layout-quad.R:169:1', 'test-layout-quad.R:300:1',
'test-layout-quad.R:345:1', 'test-layout-quad.R:499:1',
'test-layout-stack.R:37:1', 'test-layout-stack.R:49:1',
'test-layout-stack.R:77:1', 'test-layout-stack.R:125:1',
'test-layout-stack.R:169:1', 'test-layout-stack.R:185:1', 'test-link.R:1:1',
'test-link.R:44:1', 'test-mark.R:1:1', 'test-mark.R:45:1',
'test-pair-links.R:18:1', 'test-plot-align.R:1:1', 'test-plot-align.R:38:1',
'test-plot-align.R:97:1', 'test-plot-align.R:138:1',
'test-plot-align.R:174:1', 'test-plot-align.R:268:1', 'test-plot.R:7:1'
• empty test (3): 'test-layout-chain.R:239:1', 'test-layout-chain.R:242:1',
'test-layout-chain.R:246:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fortify-matrix.R:12:5'): `MAF` method calculate variant_weights ──
Error in ``[.data.table`(maf.con.class.summary, , `:=`(fract, (nVars/sum(nVars)) * 100), by = .(Tumor_Sample_Barcode))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-fortify-matrix.R:12:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::rowSums(ggalign_attr(fortify_matrix(laml), "variant_weights")[-1])
5. │ └─base::is.data.frame(x)
6. ├─ggalign::ggalign_attr(fortify_matrix(laml), "variant_weights")
7. │ └─ggalign:::ggalign_attr_get(x)
8. ├─ggalign::fortify_matrix(laml)
9. └─ggalign:::fortify_matrix.MAF(laml)
10. └─maftools::titv(data, useSyn = use_syn, plot = FALSE)
11. ├─...[]
12. └─data.table:::`[.data.table`(...)
── Error ('test-layout-heatmap.R:122:5'): `ggoncoplot()` with maftools works well ──
Error in ``[.data.table`(maf.con.class.summary, , `:=`(fract, (nVars/sum(nVars)) * 100), by = .(Tumor_Sample_Barcode))`: attempt access index 3/3 in VECTOR_ELT
Backtrace:
▆
1. ├─vdiffr::expect_doppelganger(...) at test-layout-heatmap.R:122:5
2. │ └─vdiffr (local) writer(fig, testcase, title)
3. │ └─vdiffr:::print_plot(plot, title)
4. ├─ggalign::ggoncoplot(...)
5. └─ggalign:::ggoncoplot.default(...)
6. ├─ggalign::fortify_matrix(data = data, ...)
7. └─ggalign:::fortify_matrix.MAF(data = data, ...)
8. └─maftools::titv(data, useSyn = use_syn, plot = FALSE)
9. ├─...[]
10. └─data.table:::`[.data.table`(...)
[ FAIL 2 | WARN 0 | SKIP 89 | PASS 340 ]
Deleting unused snapshots: 'layout-heatmap/gistic-oncoplot.svg',
'layout-heatmap/maf-filter-oncoplot.svg', and
'layout-heatmap/maf-pathway-oncoplot.svg'
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 1.2.0
Check: installed package size
Result: NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
R 3.0Mb
help 1.9Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64