| Back to Build/check report for BioC 3.24: simplified long |
|
This page was generated on 2026-04-29 10:01 -0400 (Wed, 29 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4843 |
| 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 2109/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.15.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for SpliceWiz in R Universe. | ||||||||||||||
|
To the developers/maintainers of the SpliceWiz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.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: SpliceWiz |
| Version: 1.15.0 |
| Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SpliceWiz |
| StartedAt: 2026-04-28 21:20:40 -0400 (Tue, 28 Apr 2026) |
| EndedAt: 2026-04-28 21:23:07 -0400 (Tue, 28 Apr 2026) |
| EllapsedTime: 147.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 SpliceWiz
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* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* preparing ‘SpliceWiz’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘SW_Cookbook.Rmd’ using rmarkdown
--- finished re-building ‘SW_Cookbook.Rmd’
--- re-building ‘SW_QuickStart.Rmd’ using rmarkdown
Quitting from SW_QuickStart.Rmd:339-347 [unnamed-chunk-16]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `c("gene_id") := genes$gene_id[match(get("gene_name"), genes$gene_name)]`:
! Check that is.data.table(DT) == TRUE. Otherwise, `:=` is defined for use in j, once only and in particular ways. See help(":=", "data.table"). A common reason for this error is allocating a new column in `j` and using `<-` instead of `:=`; e.g., `DT[, new_col <- 1]` should be `DT[, new_col := 1]`. Another is using `:=` in a multi-statement `{...}` block; please use `:=` as the only statement in `j`.
---
Backtrace:
▆
1. └─SpliceWiz::buildRef(...)
2. └─SpliceWiz:::.process_ontology(...)
3. └─c("gene_id") := ...
4. └─data.table:::stopf(...)
5. └─data.table:::raise_condition(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SW_QuickStart.Rmd' failed with diagnostics:
Check that is.data.table(DT) == TRUE. Otherwise, `:=` is defined for use in j, once only and in particular ways. See help(":=", "data.table"). A common reason for this error is allocating a new column in `j` and using `<-` instead of `:=`; e.g., `DT[, new_col <- 1]` should be `DT[, new_col := 1]`. Another is using `:=` in a multi-statement `{...}` block; please use `:=` as the only statement in `j`.
--- failed re-building ‘SW_QuickStart.Rmd’
SUMMARY: processing the following file failed:
‘SW_QuickStart.Rmd’
Error: Vignette re-building failed.
Execution halted