| Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-03-19 11:47 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 2121/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Laurent Gatto
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the synapter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/synapter.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: synapter |
| Version: 2.31.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data synapter |
| StartedAt: 2025-03-18 17:49:50 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 17:51:02 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 71.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data synapter
###
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* checking for file ‘synapter/DESCRIPTION’ ... OK
* preparing ‘synapter’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘fragmentmatching.Rmd’ using rmarkdown
2025-03-18 17:50:19.717 R[51332:750928042] XType: Using static font registry.
Quitting from fragmentmatching.Rmd:106-113 [filterfragments]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
---
Backtrace:
▆
1. ├─synapter::filterFragments(...)
2. └─synapter::filterFragments(...)
3. └─synapter (local) .local(object, ...)
4. └─object$filterFragments(...)
5. └─synapter:::.filterIntensity(...)
6. ├─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
7. └─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
8. └─MSnbase (local) .local(object, t, ...)
9. └─MSnbase:::removePeaks_MSnExp(object, t, verbose)
10. └─methods::validObject(object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'fragmentmatching.Rmd' failed with diagnostics:
invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
--- failed re-building ‘fragmentmatching.Rmd’
--- re-building ‘synapter.Rmd’ using rmarkdown
--- finished re-building ‘synapter.Rmd’
--- re-building ‘synapter2.Rmd’ using rmarkdown
Quitting from synapter2.Rmd:178-185 [filterfragments]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `validObject()`:
! invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
---
Backtrace:
▆
1. ├─synapter::filterFragments(...)
2. └─synapter::filterFragments(...)
3. └─synapter (local) .local(object, ...)
4. └─object$filterFragments(...)
5. └─synapter:::.filterIntensity(...)
6. ├─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
7. └─MSnbase::removePeaks(msexp, t = minIntensity, verbose = verbose)
8. └─MSnbase (local) .local(object, t, ...)
9. └─MSnbase:::removePeaks_MSnExp(object, t, verbose)
10. └─methods::validObject(object)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'synapter2.Rmd' failed with diagnostics:
invalid class "MSnExp" object: invalid object for slot "phenoData" in class "MSnExp": got class "NAnnotatedDataFrame", should be or extend class "AnnotatedDataFrame"
--- failed re-building ‘synapter2.Rmd’
SUMMARY: processing the following files failed:
‘fragmentmatching.Rmd’ ‘synapter2.Rmd’
Error: Vignette re-building failed.
Execution halted