ggpicrust2
Make 'PICRUSt2' Output Analysis and Visualization Easier
v2.5.10
·
Feb 12, 2026
·
MIT + file LICENSE
Description
Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <doi:10.1093/bioinformatics/btad470>.
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
ERROR
r-devel-linux-x86_64-debian-clang
tests
Running ‘testthat.R’ [35s/41s]
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")
Reading input data...
Performing pathway differential abundance analysis...
Annotating pathways...
Creating pathway error bar plots...
Plot 1 skipped (no data for method: mock_method)
ggpicrust2 analysis 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
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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-181.R
Saving _problems/test-pathway_daa-221.R
Saving _problems/test-pathway_daa-233.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)
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
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
Using column 'sample_name' as sample identifier
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[ FAIL 8 | WARN 2 | SKIP 12 | PASS 143 ]
══ Skipped tests (12) ══════════════════════════════════════════════════════════
• 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:82:3'
• 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:36:3', 'test-pathway_annotation.R:55:3'
• {enrichplot} is not installed (3): 'test-visualize_gsea.R:5:3',
'test-visualize_gsea.R:57:3', 'test-visualize_gsea.R:67:3'
• {lefser} is not installed (1): 'test-pathway_daa.R:293:3'
══ 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:180:3'): 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:180:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:220:3'): 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:220:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:232:3'): 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:232:3
2. └─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 8 | WARN 2 | SKIP 12 | PASS 143 ]
Error:
! Test failures.
Execution halted
OK
r-devel-linux-x86_64-debian-gcc
*
OK
r-devel-linux-x86_64-fedora-clang
*
OK
r-devel-linux-x86_64-fedora-gcc
*
OK
r-devel-macos-arm64
*
OK
r-devel-windows-x86_64
*
NOTE
r-oldrel-macos-arm64
package dependencies
Package suggested but not available for checking: ‘lefser’
NOTE
r-oldrel-macos-x86_64
installed package size
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 3.6Mb
extdata 1.0Mb
OK
r-oldrel-windows-x86_64
*
OK
r-patched-linux-x86_64
*
OK
r-release-linux-x86_64
*
ERROR
r-release-macos-arm64
tests
Running ‘testthat.R’ [8s/9s]
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")
Reading input data...
Performing pathway differential abundance analysis...
Annotating pathways...
Creating pathway error bar plots...
Plot 1 skipped (no data for method: mock_method)
ggpicrust2 analysis 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
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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-181.R
Saving _problems/test-pathway_daa-221.R
Saving _problems/test-pathway_daa-233.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)
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
Using column 'sample' as sample identifier
The Sample Names in order from left to right are:
S1, S2, S3, S4
The Group Levels in order from left to right are:
A, A, B, B
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
Using column 'sample_name' as sample identifier
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[ FAIL 8 | WARN 2 | SKIP 9 | PASS 151 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• 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:82:3'
• 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:36:3', 'test-pathway_annotation.R:55:3'
• {lefser} is not installed (1): 'test-pathway_daa.R:293:3'
══ 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:180:3'): 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:180:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:220:3'): 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:220:3
2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method)
── Error ('test-pathway_daa.R:232:3'): 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:232:3
2. └─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 8 | WARN 2 | SKIP 9 | PASS 151 ]
Error:
! Test failures.
Execution halted
OK
r-release-macos-x86_64
*
OK
r-release-windows-x86_64
*
Check History
ERROR 10 OK · 2 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
ERROR
r-devel-linux-x86_64-debian-clang
tests
Running ‘testthat.R’ [35s/41s] 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/bioinformati
ERROR
r-release-macos-arm64
tests
Running ‘testthat.R’ [8s/9s] 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
NOTE
r-oldrel-macos-arm64
package dependencies
Package suggested but not available for checking: ‘lefser’
NOTE
r-oldrel-macos-x86_64
installed package size
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 3.6Mb
extdata 1.0Mb
Dependency Network
Version History
new
2.5.10
Mar 9, 2026