| Back to Workflows build report for BioC 3.23 |
This page was generated on 2025-11-11 16:30 -0500 (Tue, 11 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4823 |
| 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 26/28 | Hostname | OS / Arch | INSTALL | BUILD | ||||||||
| SingscoreAMLMutations 1.27.0 (landing page) Dharmesh D. Bhuva
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | ||||||||
|
To the developers/maintainers of the SingscoreAMLMutations package: - 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: SingscoreAMLMutations |
| Version: 1.27.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations |
| StartedAt: 2025-11-11 13:11:07 -0500 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 13:12:31 -0500 (Tue, 11 Nov 2025) |
| EllapsedTime: 84.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingscoreAMLMutations
###
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* checking for file ‘SingscoreAMLMutations/DESCRIPTION’ ... OK
* preparing ‘SingscoreAMLMutations’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘workflow_transcriptional_mut_sig.Rmd’ using rmarkdown
Quitting from workflow_transcriptional_mut_sig.Rmd:183-186 [gdc_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCdownload.aux()`:
! There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
---
Backtrace:
▆
1. └─TCGAbiolinks::GDCdownload(query_rna, directory = datapath)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
6. └─TCGAbiolinks:::GDCdownload.by.chunk(...)
7. └─TCGAbiolinks:::GDCdownload.aux(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'workflow_transcriptional_mut_sig.Rmd' failed with diagnostics:
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
--- failed re-building ‘workflow_transcriptional_mut_sig.Rmd’
--- re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’ using rmarkdown
Quitting from workflow_transcriptional_mut_sig_chinese.Rmd:180-183 [gdc_download]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCdownload.aux()`:
! There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
---
Backtrace:
▆
1. └─TCGAbiolinks::GDCdownload(query_rna, directory = datapath)
2. └─base::tryCatch(...)
3. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. └─value[[3L]](cond)
6. └─TCGAbiolinks:::GDCdownload.by.chunk(...)
7. └─TCGAbiolinks:::GDCdownload.aux(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'workflow_transcriptional_mut_sig_chinese.Rmd' failed with diagnostics:
There was an error in the download process (we might had a connection problem with GDC server).
Please run this function it again.
Try using method = `client` or setting files.per.chunk to a small number.
--- failed re-building ‘workflow_transcriptional_mut_sig_chinese.Rmd’
SUMMARY: processing the following files failed:
‘workflow_transcriptional_mut_sig.Rmd’
‘workflow_transcriptional_mut_sig_chinese.Rmd’
Error: Vignette re-building failed.
Execution halted