| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-16 11:57 -0500 (Mon, 16 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 623/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DOtools 1.0.1 (landing page) Mariano Ruz Jurado
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for DOtools in R Universe. | ||||||||||||||
|
To the developers/maintainers of the DOtools package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DOtools.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: DOtools |
| Version: 1.0.1 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools |
| StartedAt: 2026-02-12 17:53:58 -0500 (Thu, 12 Feb 2026) |
| EndedAt: 2026-02-12 17:57:51 -0500 (Thu, 12 Feb 2026) |
| EllapsedTime: 233.2 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 DOtools
###
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* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘DOtools.Rmd’ using rmarkdown
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Y8bod8P `Y8bod8P' o888o o888o "888" .8' 888bod8P' o888o 8""888P' "888"
.o..P' 888
`Y8P' o888o @Teichmann lab
⚙️ Configuration:
🛠️ indata: /tmp/Rtmp2lbiaG/file5d58f60b86d23/ad.h5ad
🛠️ model: Healthy_COVID19_PBMC.pkl
🛠️ transpose-input: False
🛠️ gene-file: None
🛠️ cell-file: None
🛠️ mode: best_match
🛠️ p-thres: 0.5
🛠️ majority-voting: True
🛠️ outdir: /tmp/Rtmp2lbiaG/file5d58f60b86d23
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: leiden0.3
🛠️ min-prop: 0.0
📁 Input file is '/tmp/Rtmp2lbiaG/file5d58f60b86d23/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 2807 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!
[INFO] Your data doesn't have replicates! Artificial replicates will be simulated to run scanpro.
[INFO] Simulation may take some minutes...
[INFO] Generating 3 replicates and running 100 simulations...
[INFO] Finished 100 simulations in 3.9 seconds
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888 888 .o8 `"' .o8
.ooooo. .ooooo. 888 888 .o888oo oooo ooo oo.ooooo. oooo .oooo.o .o888oo
d88' "Y8 d88 88b 888 888 888 88. .8 888 88b 888 d88( "8 888
888 888ooo888 888 888 888 88..8 888 888 888 `"Y88b. 888
888 .o8 888 .o 888 888 888 . `888' 888 888 888 o. )88b 888 .
Y8bod8P `Y8bod8P' o888o o888o "888" .8' 888bod8P' o888o 8""888P' "888"
.o..P' 888
`Y8P' o888o @Teichmann lab
⚙️ Configuration:
🛠️ indata: /tmp/Rtmp2lbiaG/file5d58f1fb5706b/ad.h5ad
🛠️ model: Healthy_COVID19_PBMC.pkl
🛠️ transpose-input: False
🛠️ gene-file: None
🛠️ cell-file: None
🛠️ mode: best_match
🛠️ p-thres: 0.5
🛠️ majority-voting: True
🛠️ outdir: /tmp/Rtmp2lbiaG/file5d58f1fb5706b
🛠️ prefix:
🛠️ xlsx: False
🛠️ plot-results: False
🛠️ quiet: False
🛠️ over-clustering: annotation_recluster
🛠️ min-prop: 0.0
📁 Input file is '/tmp/Rtmp2lbiaG/file5d58f1fb5706b/ad.h5ad'
⏳ Loading data
⚠️ Warning: invalid expression matrix, expect ALL genes and log1p normalized expression to 10000 counts per cell. The prediction result may not be accurate
🔬 Input data has 1799 cells and 800 genes
🔗 Matching reference genes in the model
🧬 609 features used for prediction
⚖️ Scaling input data
🖋️ Predicting labels
✅ Prediction done!
🗳️ Majority voting the predictions
✅ Majority voting done!
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!!! Assuming GO Terms are preprocessed (Only Significant terms included)
Quitting from DOtools.Rmd:648-660 [Bar]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `DO.BarplotWilcox()`:
! could not find function "DO.BarplotWilcox"
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'DOtools.Rmd' failed with diagnostics:
could not find function "DO.BarplotWilcox"
--- failed re-building ‘DOtools.Rmd’
SUMMARY: processing the following file failed:
‘DOtools.Rmd’
Error: Vignette re-building failed.
Execution halted