Ying Chen
| Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024) |
| git_url: https://git.bioconductor.org/packages/bambu |
| git_branch: devel |
| git_last_commit: 65fb8df |
| git_last_commit_date: 2024-04-30 11:28:33 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-07-24 11:39 -0400 (Wed, 24 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4688 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4284 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4404 |
| 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 124/2248 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| bambu 3.7.0 (landing page) Ying Chen
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the bambu package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bambu.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: bambu |
| Version: 3.7.0 |
| Command: chmod a+r bambu -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data bambu |
| StartedAt: 2024-07-23 16:57:47 -0400 (Tue, 23 Jul 2024) |
| EndedAt: 2024-07-23 17:13:27 -0400 (Tue, 23 Jul 2024) |
| EllapsedTime: 940.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
###
### chmod a+r bambu -R && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data bambu
###
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* checking for file 'bambu/DESCRIPTION' ... OK
* preparing 'bambu':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'bambu.Rmd' using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
Warning in eng_r(options) :
Failed to tidy R code in chunk 'unnamed-chunk-35'. Reason:
Error in base::parse(text = code, keep.source = keep.source) :
<text>:16:15: unexpected ','
15:
16: rcFile <- NULL,
^
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc249b560f_3845'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc30571542_3847'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffceeb34e_3849'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc4cb47f68_3851'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc35495cdd_3853'
[E::idx_find_and_load] Could not retrieve index file for 'F:\biocbuild\ExperimentHub_cache/ffc6474635a_3855'
Quitting from lines 404-411 [unnamed-chunk-37] (bambu.Rmd)
Error: processing vignette 'bambu.Rmd' failed with diagnostics:
there is no package called 'DESeq2'
--- failed re-building 'bambu.Rmd'
SUMMARY: processing the following file failed:
'bambu.Rmd'
Error: Vignette re-building failed.
Execution halted