Last updated on 2026-08-03 14:50:50 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 | 10.17 | 154.35 | 164.52 | 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 | 221.00 | 237.00 | OK | |
| r-oldrel-macos-arm64 | 2.5.17 | 3.00 | 67.00 | 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 | 25.00 | 278.00 | 303.00 | 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:
‘~/tmp/scratch/Rtmp0FU9t0’ ‘~/tmp/scratch/Rtmp0OWboQ’
‘~/tmp/scratch/Rtmp0Zn13I’ ‘~/tmp/scratch/Rtmp0oJjS5’
‘~/tmp/scratch/Rtmp1ELsuD’ ‘~/tmp/scratch/Rtmp1NdvRt’
‘~/tmp/scratch/Rtmp1YtP3C’ ‘~/tmp/scratch/Rtmp2VHwdP’
‘~/tmp/scratch/Rtmp33fPxY’ ‘~/tmp/scratch/Rtmp3RVt6g’
‘~/tmp/scratch/Rtmp3U7Eqi’ ‘~/tmp/scratch/Rtmp3kPCq3’
‘~/tmp/scratch/Rtmp4OG0rL’ ‘~/tmp/scratch/Rtmp4dzx1E’
‘~/tmp/scratch/Rtmp4rMkFM’ ‘~/tmp/scratch/Rtmp4t6Cvv’
‘~/tmp/scratch/Rtmp4ygFZi’ ‘~/tmp/scratch/Rtmp559aRN’
‘~/tmp/scratch/Rtmp5At566’ ‘~/tmp/scratch/Rtmp5JNP7d’
‘~/tmp/scratch/Rtmp5gk95N’ ‘~/tmp/scratch/Rtmp6IMYx7’
‘~/tmp/scratch/Rtmp6eaZ98’ ‘~/tmp/scratch/Rtmp6l7yJJ’
‘~/tmp/scratch/Rtmp79mA7t’ ‘~/tmp/scratch/Rtmp7GXtnd’
‘~/tmp/scratch/Rtmp7RjsKC’ ‘~/tmp/scratch/Rtmp7ZlblE’
‘~/tmp/scratch/Rtmp7lBZQ9’ ‘~/tmp/scratch/Rtmp82yS8L’
‘~/tmp/scratch/Rtmp8em9ck’ ‘~/tmp/scratch/Rtmp9KQCr9’
‘~/tmp/scratch/Rtmp9kSVos’ ‘~/tmp/scratch/RtmpA02w3f’
‘~/tmp/scratch/RtmpAdbfgB’ ‘~/tmp/scratch/RtmpAhNIJ9’
‘~/tmp/scratch/RtmpBshBRz’ ‘~/tmp/scratch/RtmpC0b1mE’
‘~/tmp/scratch/RtmpCDDqIQ’ ‘~/tmp/scratch/RtmpDP3wCC’
‘~/tmp/scratch/RtmpDp2mHw’ ‘~/tmp/scratch/RtmpEuKQL3’
‘~/tmp/scratch/RtmpF21TqI’ ‘~/tmp/scratch/RtmpFFVAdw’
‘~/tmp/scratch/RtmpFNLGG1’ ‘~/tmp/scratch/RtmpFmlTNO’
‘~/tmp/scratch/RtmpG2F7m3’ ‘~/tmp/scratch/RtmpG30RFD’
‘~/tmp/scratch/RtmpGfl6ql’ ‘~/tmp/scratch/RtmpGlnMjm’
‘~/tmp/scratch/RtmpHSkrfM’ ‘~/tmp/scratch/RtmpHfEs8c’
‘~/tmp/scratch/RtmpHpUEjf’ ‘~/tmp/scratch/RtmpI4OCTO’
‘~/tmp/scratch/RtmpIOol0d’ ‘~/tmp/scratch/RtmpJHwUst’
‘~/tmp/scratch/RtmpJVqw3u’ ‘~/tmp/scratch/RtmpJau2cO’
‘~/tmp/scratch/RtmpJrRffg’ ‘~/tmp/scratch/RtmpK9xiQ6’
‘~/tmp/scratch/RtmpKezamW’ ‘~/tmp/scratch/RtmpLHaAXE’
‘~/tmp/scratch/RtmpLTwXo5’ ‘~/tmp/scratch/RtmpLen2r8’
‘~/tmp/scratch/RtmpM3rMlB’ ‘~/tmp/scratch/RtmpM4e6H6’
‘~/tmp/scratch/RtmpMRLCKL’ ‘~/tmp/scratch/RtmpMWVvei’
‘~/tmp/scratch/RtmpMdpYvk’ ‘~/tmp/scratch/RtmpNU5Wqx’
‘~/tmp/scratch/RtmpNcuCqG’ ‘~/tmp/scratch/RtmpO0oRtb’
‘~/tmp/scratch/RtmpO3Upw1’ ‘~/tmp/scratch/RtmpOAViXP’
‘~/tmp/scratch/RtmpOInvtR’ ‘~/tmp/scratch/RtmpOsd1VH’
‘~/tmp/scratch/RtmpPWDrRk’ ‘~/tmp/scratch/RtmpQgfnUg’
‘~/tmp/scratch/RtmpQqyQxt’ ‘~/tmp/scratch/RtmpQzgMh4’
‘~/tmp/scratch/RtmpRELGtI’ ‘~/tmp/scratch/RtmpRky3vc’
‘~/tmp/scratch/RtmpTGNM5i’ ‘~/tmp/scratch/RtmpTIhrfR’
‘~/tmp/scratch/RtmpTVKNUf’ ‘~/tmp/scratch/RtmpTYme5G’
‘~/tmp/scratch/RtmpTsqH23’ ‘~/tmp/scratch/RtmpUCtFmg’
‘~/tmp/scratch/RtmpUhvnhR’ ‘~/tmp/scratch/RtmpVr7aA5’
‘~/tmp/scratch/RtmpVuqf73’ ‘~/tmp/scratch/RtmpWR4v7y’
‘~/tmp/scratch/RtmpWWteIs’ ‘~/tmp/scratch/RtmpWcchwD’
‘~/tmp/scratch/RtmpWjzXeB’ ‘~/tmp/scratch/RtmpX6NywU’
‘~/tmp/scratch/RtmpXGGxJY’ ‘~/tmp/scratch/RtmpXz0D8i’
‘~/tmp/scratch/RtmpY0HHMB’ ‘~/tmp/scratch/RtmpYWiGmk’
‘~/tmp/scratch/RtmpZAvqPA’ ‘~/tmp/scratch/RtmpZtfHrD’
‘~/tmp/scratch/RtmpaFlQul’ ‘~/tmp/scratch/Rtmpae8Anq’
‘~/tmp/scratch/RtmpanE9dh’ ‘~/tmp/scratch/RtmpapV69y’
‘~/tmp/scratch/RtmpbG1YZS’ ‘~/tmp/scratch/RtmpbVqChL’
‘~/tmp/scratch/RtmpbXH56H’ ‘~/tmp/scratch/RtmpbvSx4Z’
‘~/tmp/scratch/Rtmpc6oMq6’ ‘~/tmp/scratch/RtmpcKXpxD’
‘~/tmp/scratch/RtmpcU91T4’ ‘~/tmp/scratch/RtmpcdwvwD’
‘~/tmp/scratch/Rtmpd6nDZl’ ‘~/tmp/scratch/RtmpdQtIHa’
‘~/tmp/scratch/Rtmpe2vFol’ ‘~/tmp/scratch/Rtmpe5dUV5’
‘~/tmp/scratch/Rtmpe5gpma’ ‘~/tmp/scratch/RtmpeTHcQA’
‘~/tmp/scratch/RtmpegsfiS’ ‘~/tmp/scratch/Rtmpf4IHwn’
‘~/tmp/scratch/RtmpfSzVw6’ ‘~/tmp/scratch/RtmpfVPGWW’
‘~/tmp/scratch/RtmpfVqncL’ ‘~/tmp/scratch/Rtmpg1WiiS’
‘~/tmp/scratch/RtmpgBeVw3’ ‘~/tmp/scratch/RtmpgBxXGx’
‘~/tmp/scratch/RtmpgJjo2Y’ ‘~/tmp/scratch/Rtmph2EnOg’
‘~/tmp/scratch/Rtmph88PlM’ ‘~/tmp/scratch/RtmphbpkgL’
‘~/tmp/scratch/RtmphssFBo’ ‘~/tmp/scratch/Rtmpht9Dr2’
‘~/tmp/scratch/RtmpiIZTnO’ ‘~/tmp/scratch/Rtmpift2TO’
‘~/tmp/scratch/Rtmpka5DSi’ ‘~/tmp/scratch/Rtmpkhat2m’
‘~/tmp/scratch/Rtmpl7xNLZ’ ‘~/tmp/scratch/RtmpleCYR3’
‘~/tmp/scratch/RtmplmmlNY’ ‘~/tmp/scratch/Rtmplq00WA’
‘~/tmp/scratch/Rtmpm6pUj5’ ‘~/tmp/scratch/RtmpnPwqi9’
‘~/tmp/scratch/Rtmpnpzipq’ ‘~/tmp/scratch/RtmpoYqIzF’
‘~/tmp/scratch/RtmpoeiMnK’ ‘~/tmp/scratch/RtmpozyLFu’
‘~/tmp/scratch/RtmppY2lR1’ ‘~/tmp/scratch/RtmppqbA8f’
‘~/tmp/scratch/Rtmpq2d1OV’ ‘~/tmp/scratch/RtmpqPvEMY’
‘~/tmp/scratch/Rtmpqq01uo’ ‘~/tmp/scratch/Rtmpqrk9ti’
‘~/tmp/scratch/Rtmpr37BON’ ‘~/tmp/scratch/RtmprCNgA7’
‘~/tmp/scratch/RtmprPs4Pa’ ‘~/tmp/scratch/RtmpsNB5aZ’
‘~/tmp/scratch/RtmpsRBf1V’ ‘~/tmp/scratch/RtmpsZ1Hg0’
‘~/tmp/scratch/RtmpswBSRo’ ‘~/tmp/scratch/RtmptY1xUT’
‘~/tmp/scratch/RtmpvFB30F’ ‘~/tmp/scratch/RtmpvnshUP’
‘~/tmp/scratch/RtmpvqHiAx’ ‘~/tmp/scratch/Rtmpw0XzOh’
‘~/tmp/scratch/RtmpzDFcDT’ ‘~/tmp/scratch/RtmpzFwFsG’
‘~/tmp/scratch/RtmpzRhmAJ’ ‘~/tmp/scratch/RtmpzmVB9b’
‘~/tmp/scratch/quarto-session22e791f4631afd4d’
‘~/tmp/scratch/quarto-sessiondc0da37eb1654d1d’
‘~/tmp/scratch/xvfb-run.0Xjh5Q’ ‘~/tmp/scratch/xvfb-run.0tLWQ2’
‘~/tmp/scratch/xvfb-run.13YpA3’ ‘~/tmp/scratch/xvfb-run.215XPj’
‘~/tmp/scratch/xvfb-run.4HTL3T’ ‘~/tmp/scratch/xvfb-run.4b77kT’
‘~/tmp/scratch/xvfb-run.4hEawh’ ‘~/tmp/scratch/xvfb-run.4j0jxM’
‘~/tmp/scratch/xvfb-run.4z5B41’ ‘~/tmp/scratch/xvfb-run.7HjDwb’
‘~/tmp/scratch/xvfb-run.CCdjpV’ ‘~/tmp/scratch/xvfb-run.DUrf33’
‘~/tmp/scratch/xvfb-run.DYTSqI’ ‘~/tmp/scratch/xvfb-run.DbxpC3’
‘~/tmp/scratch/xvfb-run.DhSXaC’ ‘~/tmp/scratch/xvfb-run.Fv342x’
‘~/tmp/scratch/xvfb-run.GrIeT2’ ‘~/tmp/scratch/xvfb-run.HRvwCd’
‘~/tmp/scratch/xvfb-run.I5X1Gr’ ‘~/tmp/scratch/xvfb-run.JdEjiQ’
‘~/tmp/scratch/xvfb-run.JnnAVv’ ‘~/tmp/scratch/xvfb-run.Keo3ma’
‘~/tmp/scratch/xvfb-run.LgrMuN’ ‘~/tmp/scratch/xvfb-run.MjG2V9’
‘~/tmp/scratch/xvfb-run.NoZDH7’ ‘~/tmp/scratch/xvfb-run.OLLE9B’
‘~/tmp/scratch/xvfb-run.Olkvld’ ‘~/tmp/scratch/xvfb-run.PmGSc4’
‘~/tmp/scratch/xvfb-run.RUk2CG’ ‘~/tmp/scratch/xvfb-run.SIVuOk’
‘~/tmp/scratch/xvfb-run.SSLkCx’ ‘~/tmp/scratch/xvfb-run.T0YqLW’
‘~/tmp/scratch/xvfb-run.UBQybP’ ‘~/tmp/scratch/xvfb-run.UsQT88’
‘~/tmp/scratch/xvfb-run.WPXllE’ ‘~/tmp/scratch/xvfb-run.XI7OjB’
‘~/tmp/scratch/xvfb-run.ZyfRSW’ ‘~/tmp/scratch/xvfb-run.aZRiiC’
‘~/tmp/scratch/xvfb-run.bFXsuf’ ‘~/tmp/scratch/xvfb-run.dGc0Sa’
‘~/tmp/scratch/xvfb-run.dOO8Nh’ ‘~/tmp/scratch/xvfb-run.fuI44c’
‘~/tmp/scratch/xvfb-run.gPrFeQ’ ‘~/tmp/scratch/xvfb-run.h2PZVl’
‘~/tmp/scratch/xvfb-run.i5tUxl’ ‘~/tmp/scratch/xvfb-run.icvFud’
‘~/tmp/scratch/xvfb-run.j93jC7’ ‘~/tmp/scratch/xvfb-run.m1ILnI’
‘~/tmp/scratch/xvfb-run.mOBDgB’ ‘~/tmp/scratch/xvfb-run.myR1gG’
‘~/tmp/scratch/xvfb-run.pJF7Jx’ ‘~/tmp/scratch/xvfb-run.q8jAMU’
‘~/tmp/scratch/xvfb-run.quUnum’ ‘~/tmp/scratch/xvfb-run.rIYVfj’
‘~/tmp/scratch/xvfb-run.rUibbY’ ‘~/tmp/scratch/xvfb-run.sJVD0s’
‘~/tmp/scratch/xvfb-run.tOtAei’ ‘~/tmp/scratch/xvfb-run.tXAV1v’
‘~/tmp/scratch/xvfb-run.tvMBZ7’ ‘~/tmp/scratch/xvfb-run.utFvjk’
‘~/tmp/scratch/xvfb-run.uuQlrp’ ‘~/tmp/scratch/xvfb-run.v2JEfI’
‘~/tmp/scratch/xvfb-run.vITX9s’ ‘~/tmp/scratch/xvfb-run.vXRsyF’
‘~/tmp/scratch/xvfb-run.vfXGv9’ ‘~/tmp/scratch/xvfb-run.yE3Gbd’
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.5.17
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/22s]
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