Last updated on 2026-08-04 07:50:40 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.5.17 | 14.19 | 223.76 | 237.95 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.5.17 | 10.06 | 153.26 | 163.32 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.5.17 | 18.00 | 197.26 | 215.26 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.5.17 | 157.93 | OK | |||
| r-devel-windows-x86_64 | 2.5.17 | 19.00 | 216.00 | 235.00 | OK | |
| r-patched-linux-x86_64 | 2.5.17 | 13.40 | 203.76 | 217.16 | OK | |
| r-release-linux-x86_64 | 2.5.17 | 14.38 | 204.47 | 218.85 | OK | |
| r-release-macos-arm64 | 2.5.17 | 4.00 | 71.00 | 75.00 | OK | |
| r-release-macos-x86_64 | 2.5.17 | 11.00 | 291.00 | 302.00 | OK | |
| r-release-windows-x86_64 | 2.5.17 | 16.00 | 215.00 | 231.00 | OK | |
| r-oldrel-macos-arm64 | 2.5.17 | 4.00 | 66.00 | 70.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.5.17 | 10.00 | 309.00 | 319.00 | OK | |
| r-oldrel-windows-x86_64 | 2.5.17 | 22.00 | 285.00 | 307.00 | OK |
Version: 2.5.17
Check: Rd contents
Result: NOTE
Rd files without \usage:
‘compare_daa_results.Rd’ ‘pathway_errorbar.Rd’ ‘pathway_heatmap.Rd’
\arguments should not be documented without \usage.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.5.17
Check: for new files in some other directories
Result: NOTE
Found the following files/directories:
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‘~/tmp/scratch/Rtmp0aUx68’ ‘~/tmp/scratch/Rtmp0fhb5y’
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‘~/tmp/scratch/RtmpAGEkUX’ ‘~/tmp/scratch/RtmpAy8Uaa’
‘~/tmp/scratch/RtmpB0GGnG’ ‘~/tmp/scratch/RtmpBrsBKP’
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‘~/tmp/scratch/RtmpYEkgni’ ‘~/tmp/scratch/RtmpYbvdu0’
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‘~/tmp/scratch/RtmpZdetl4’ ‘~/tmp/scratch/RtmpZsCpO1’
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‘~/tmp/scratch/RtmpjrrDVR’ ‘~/tmp/scratch/RtmpkFX3ll’
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‘~/tmp/scratch/RtmplHPsLE’ ‘~/tmp/scratch/RtmplRjZSJ’
‘~/tmp/scratch/Rtmplf5TYY’ ‘~/tmp/scratch/Rtmplh4Ceg’
‘~/tmp/scratch/RtmpltMr2S’ ‘~/tmp/scratch/RtmplwG4B7’
‘~/tmp/scratch/RtmpmOfyft’ ‘~/tmp/scratch/RtmpmUXiBn’
‘~/tmp/scratch/Rtmpn5GEAI’ ‘~/tmp/scratch/RtmpnEuYFF’
‘~/tmp/scratch/RtmpnPwbCB’ ‘~/tmp/scratch/RtmpotfK4g’
‘~/tmp/scratch/Rtmpp6MsJq’ ‘~/tmp/scratch/RtmppJowcs’
‘~/tmp/scratch/RtmppUMAVA’ ‘~/tmp/scratch/RtmpqHzMNY’
‘~/tmp/scratch/RtmpqLu28n’ ‘~/tmp/scratch/RtmprCTBfL’
‘~/tmp/scratch/RtmprMueyR’ ‘~/tmp/scratch/Rtmps7DdyV’
‘~/tmp/scratch/RtmpsSeqy8’ ‘~/tmp/scratch/RtmpsTe7W6’
‘~/tmp/scratch/RtmpsXfKNE’ ‘~/tmp/scratch/RtmpsbIlaH’
‘~/tmp/scratch/RtmpsdGhcz’ ‘~/tmp/scratch/Rtmpsf1DUX’
‘~/tmp/scratch/RtmptbIPo7’ ‘~/tmp/scratch/Rtmpu6V8Iq’
‘~/tmp/scratch/Rtmpv3oSsl’ ‘~/tmp/scratch/RtmpvbQMVU’
‘~/tmp/scratch/Rtmpwd5DDB’ ‘~/tmp/scratch/RtmpxOvqHG’
‘~/tmp/scratch/Rtmpy0nbkM’ ‘~/tmp/scratch/Rtmpy8ZiLD’
‘~/tmp/scratch/RtmpyEHM0V’ ‘~/tmp/scratch/RtmpyI7fAq’
‘~/tmp/scratch/quarto-sessiona11e0f92ffa93da9’
‘~/tmp/scratch/xvfb-run.0fNYbK’ ‘~/tmp/scratch/xvfb-run.0lBTbq’
‘~/tmp/scratch/xvfb-run.1VKG6B’ ‘~/tmp/scratch/xvfb-run.2fn5JK’
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‘~/tmp/scratch/xvfb-run.AFk4X2’ ‘~/tmp/scratch/xvfb-run.Bqv7v6’
‘~/tmp/scratch/xvfb-run.CZoSB9’ ‘~/tmp/scratch/xvfb-run.D5d8hO’
‘~/tmp/scratch/xvfb-run.D8gJgw’ ‘~/tmp/scratch/xvfb-run.EKk1ib’
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‘~/tmp/scratch/xvfb-run.EeUNuq’ ‘~/tmp/scratch/xvfb-run.EsRAeE’
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‘~/tmp/scratch/xvfb-run.NldRPe’ ‘~/tmp/scratch/xvfb-run.OfT2mZ’
‘~/tmp/scratch/xvfb-run.Ogqv42’ ‘~/tmp/scratch/xvfb-run.PKKFuV’
‘~/tmp/scratch/xvfb-run.QihCGy’ ‘~/tmp/scratch/xvfb-run.QvEZpe’
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‘~/tmp/scratch/xvfb-run.TAmGKy’ ‘~/tmp/scratch/xvfb-run.TdJ56m’
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‘~/tmp/scratch/xvfb-run.Yi0NhI’ ‘~/tmp/scratch/xvfb-run.ZNmlHS’
‘~/tmp/scratch/xvfb-run.cB4N2z’ ‘~/tmp/scratch/xvfb-run.cLnpZo’
‘~/tmp/scratch/xvfb-run.e4uE8q’ ‘~/tmp/scratch/xvfb-run.eCytDU’
‘~/tmp/scratch/xvfb-run.giNsuS’ ‘~/tmp/scratch/xvfb-run.iPUdqO’
‘~/tmp/scratch/xvfb-run.j6Cof6’ ‘~/tmp/scratch/xvfb-run.jfONXA’
‘~/tmp/scratch/xvfb-run.l6uF4Y’ ‘~/tmp/scratch/xvfb-run.nhXsNC’
‘~/tmp/scratch/xvfb-run.oiVQn2’ ‘~/tmp/scratch/xvfb-run.pJNBAm’
‘~/tmp/scratch/xvfb-run.r5C2uA’ ‘~/tmp/scratch/xvfb-run.ucPsFq’
‘~/tmp/scratch/xvfb-run.v5jmWA’ ‘~/tmp/scratch/xvfb-run.vLCP0a’
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‘~/tmp/scratch/xvfb-run.xFGTtm’ ‘~/tmp/scratch/xvfb-run.xI9rxO’
‘~/tmp/scratch/xvfb-run.xdrtdL’ ‘~/tmp/scratch/xvfb-run.xil9Mn’
‘~/tmp/scratch/xvfb-run.zXwQse’ ‘~/tmp/scratch/xvfb-run.zcseCn’
‘~/tmp/scratch/xvfb-run.zhu52g’ ‘~/tmp/scratch/xvfb-run.zwzwm6’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.5.17
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggpicrust2)
Loading required package: ggpicrust2
To cite ggpicrust2 in publications use:
Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, Liangliang Zhang, ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization, Bioinformatics, Volume 39, Issue 8, August 2023, btad470, https://doi.org/10.1093/bioinformatics/btad470
>
> test_check("ggpicrust2")
0 features are filtered!
The filtered data has 12 samples and 20 features will be tested!
Pseudo-count approach is used.
Fit linear models ...
Completed.
0 features are filtered!
The filtered data has 12 samples and 20 features will be tested!
Pseudo-count approach is used.
Fit linear models ...
Completed.
0 features are filtered!
The filtered data has 6 samples and 15 features will be tested!
Pseudo-count approach is used.
Fit linear models ...
Completed.
Using column 'sample' as sample identifier
1 constant pathway(s) have zero variance; treated as z-score 0 for clustering.
Samples ordered by group (4 samples, 2 groups)
Pathways ordered by hierarchical clustering (complete method, euclidean distance)
Reading input data...
Annotating pathways...
Creating pathway error bar plots...
Plot 1 skipped (no data for method: mock_method)
ggpicrust2 analysis completed.
0 features are filtered!
The filtered data has 8 samples and 15 features will be tested!
Fit linear models ...
Completed.
Reading input data...
Annotating pathways...
Creating pathway error bar plots...
Plot 1 skipped (no data for method: mock_method)
ggpicrust2 analysis completed.
0 features are filtered!
The filtered data has 6 samples and 10 features will be tested!
Fit linear models ...
Completed.
Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference.
Using column 'sample_name' as sample identifier
Saving _problems/test-pathway_daa-32.R
Saving _problems/test-pathway_daa-52.R
Saving _problems/test-pathway_daa-86.R
Saving _problems/test-pathway_daa-150.R
Saving _problems/test-pathway_daa-188.R
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
All dispersion fitting methods failed, using gene-wise estimates...
converting counts to integer mode
it appears that the last variable in the design formula, 'group',
has a factor level, 'control', which is not the reference level. we recommend
to use factor(...,levels=...) or relevel() to set this as the reference level
before proceeding. for more information, please see the 'Note on factor levels'
in vignette('DESeq2').
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
All dispersion fitting methods failed, using gene-wise estimates...
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
gene-wise dispersion estimates
mean-dispersion relationship
All dispersion fitting methods failed, using gene-wise estimates...
Saving _problems/test-pathway_daa-419.R
Saving _problems/test-pathway_daa-441.R
Saving _problems/test-pathway_daa-499.R
Saving _problems/test-pathway_daa-523.R
Saving _problems/test-pathway_daa-552.R
Saving _problems/test-pathway_daa-577.R
0 features are filtered!
The filtered data has 12 samples and 12 features will be tested!
Fit linear models ...
Completed.
0 features are filtered!
The filtered data has 12 samples and 12 features will be tested!
Fit linear models ...
Completed.
Disp = 1e-04 , BCV = 0.01
Disp = 1e-04 , BCV = 0.01
Saving _problems/test-pathway_daa-858.R
Excluded 1 pathways with missing annotations. Use 'pathway_annotation' to add them.
Excluded 1 rows with missing 'pathway_name' annotations.
Saving _problems/test-pathway_errorbar-232.R
Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference.
Using column 'sample_name' as sample identifier
Using column 'sample_name' as sample identifier
Testing 2 gene sets (filtered from 2 by size constraints)
Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference.
Using column 'sample' as sample identifier
Using column 'sample' as sample identifier
Samples ordered by group (4 samples, 2 groups)
Using column 'sample' as sample identifier
Samples ordered by group (4 samples, 2 groups)
Using column 'sample' as sample identifier
Samples ordered by group (4 samples, 2 groups)
Using column 'sample_name' as sample identifier
Using column 'sample_name' as sample identifier
Using column 'sample_name' as sample identifier
Too few points to calculate an ellipse
Too few points to calculate an ellipse
Using column 'sample_name' as sample identifier
Using column 'sample_name' as sample identifier
Using column 'sample_name' as sample identifier
[ FAIL 13 | WARN 3 | SKIP 17 | PASS 453 ]
══ Skipped tests (17) ══════════════════════════════════════════════════════════
• On CRAN (4): 'test-pathway_ridgeplot.R:25:3',
'test-pathway_ridgeplot.R:42:3', 'test-pathway_ridgeplot.R:65:3',
'test-pathway_volcano.R:111:3'
• Set GGPICRUST2_RUN_E2E_TESTS=true to run full ggpicrust2 end-to-end tests.
(1): 'test-ggpicrust2-return-structure.R:4:3'
• Set GGPICRUST2_RUN_EXTENDED_DAA_TESTS=true to run extended DAA method tests.
(1): 'test-pathway_daa.R:102:3'
• Set GGPICRUST2_RUN_NETWORK_TESTS=true to run network-dependent KEGG tests.
(2): 'test-pathway_annotation.R:120:3', 'test-pathway_annotation.R:139:3'
• empty test (1): 'test-pathway_annotation.R:273:1'
• {ALDEx2} is not installed (1): 'test-pathway_daa.R:906:3'
• {Maaslin2} is not installed (2): 'test-pathway_daa.R:300:3',
'test-pathway_daa.R:683:3'
• {lefser} is not installed (1): 'test-pathway_daa.R:625:3'
• {metagenomeSeq} is not installed (4): 'test-pathway_daa.R:335:3',
'test-pathway_daa.R:371:3', 'test-pathway_daa.R:757:3',
'test-pathway_daa.R:795:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-pathway_daa.R:32:3'): pathway_daa works with basic inputs ──────
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(td$abundance, td$metadata, "group", daa_method = "ALDEx2") at test-pathway_daa.R:32:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:49:3'): pathway_daa validates inputs correctly ───
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pathway_daa.R:49:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ggpicrust2::pathway_daa(...)
8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:86:5'): pathway_daa core methods produce expected results ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. ├─base::suppressWarnings(...) at test-pathway_daa.R:86:5
2. │ └─base::withCallingHandlers(...)
3. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = method)
4. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:149:3'): pathway_daa handles sample selection correctly ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:149:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:187:3'): pathway_daa select= keeps metadata rows aligned with abundance columns ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:187:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:416:3'): pathway_daa rejects negative abundance values ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pathway_daa.R:416:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = "ALDEx2")
8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:440:3'): pathway_daa handles factor levels correctly with subset ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:440:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:498:3'): pathway_daa handles p-value adjustment correctly ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:498:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:520:3'): pathway_daa include_abundance_stats parameter works correctly ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:520:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:551:3'): ALDEx2 returns effect size columns by default ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(td$abundance, td$metadata, "group", daa_method = "ALDEx2") at test-pathway_daa.R:551:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:574:3'): include_abundance_stats does not collide with method-native log2FC ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:574:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:849:3'): pathway_daa re-validates group count after align/select ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pathway_daa.R:849:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─ggpicrust2::pathway_daa(...)
8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_errorbar.R:227:3'): pathway_errorbar_table function works correctly ──
Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2')
Backtrace:
▆
1. └─ggpicrust2::pathway_daa(...) at test-pathway_errorbar.R:227:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
[ FAIL 13 | WARN 3 | SKIP 17 | PASS 453 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-arm64