Last updated on 2026-04-21 17:53:49 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.3 | 64.44 | 826.08 | 890.52 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.1.3 | 45.87 | 500.66 | 546.53 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.1.3 | 120.00 | 1392.48 | 1512.48 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.3 | 121.00 | 1738.04 | 1859.04 | OK | |
| r-devel-macos-arm64 | 0.1.3 | 16.00 | 207.00 | 223.00 | ERROR | |
| r-devel-windows-x86_64 | 0.1.3 | 31.00 | 9.00 | 40.00 | ERROR | |
| r-patched-linux-x86_64 | 0.1.3 | 64.94 | 792.45 | 857.39 | OK | |
| r-release-linux-x86_64 | 0.1.3 | 62.94 | 528.14 | 591.08 | OK | |
| r-release-macos-arm64 | 0.1.3 | 16.00 | 173.00 | 189.00 | OK | |
| r-release-macos-x86_64 | 0.1.3 | 47.00 | 466.00 | 513.00 | OK | |
| r-release-windows-x86_64 | 0.1.3 | 90.00 | 513.00 | 603.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.3 | 7.00 | 17.00 | 24.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.1.3 | 47.00 | 626.00 | 673.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.1.3 | 114.00 | 698.00 | 812.00 | OK |
Version: 0.1.3
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘XYomics_bulk_example.Rmd’ using rmarkdown
Quitting from XYomics_bulk_example.Rmd:206-240 [pathway-analysis]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `get()`:
! invalid 'envir' argument
---
Backtrace:
▆
1. └─XYomics::improved_pathway_enrichment(...)
2. └─clusterProfiler::enrichGO(...)
3. └─clusterProfiler:::add_GO_Ontology(res, GO_DATA)
4. └─base::get("GO2ONT", envir = GO_DATA)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'XYomics_bulk_example.Rmd' failed with diagnostics:
invalid 'envir' argument
--- failed re-building ‘XYomics_bulk_example.Rmd’
--- re-building ‘XYomics_sc_example.Rmd’ using rmarkdown
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
|
| | 0%
|
|======================================================================| 100%
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
--- finished re-building ‘XYomics_sc_example.Rmd’
SUMMARY: processing the following file failed:
‘XYomics_bulk_example.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-macos-arm64
Version: 0.1.3
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-windows-x86_64, r-oldrel-macos-arm64
Version: 0.1.3
Check: installed package size
Result: NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
doc 2.1Mb
libs 2.2Mb
Flavor: r-oldrel-macos-x86_64