Hello, I am the maintainer of the wiggleplotr package and I have an error in the vignette that I cannot seem to figure out. When I look at the build report ( https://bioconductor.org/checkResults/devel/bioc-LATEST/wiggleplotr/nebbiolo2-buildsrc.html) I see the following error: Quitting from wiggleplotr.Rmd:65-67 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `plotTranscripts()`: ! object 'ccds' not found --- Backtrace: ? 1. ??wiggleplotr::plotTranscripts(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I can reproduce this error when I run R CMD build on my computer. However, when I try to debug the code interactively in R then everything works fine. I've not made any changes to the code or the package data outside the vignette. Is there something obvious that I am missing? Best, Kaur
[Bioc-devel] wiggleplotr vignette build fails with R CMD build
3 messages · Vincent Carey, Kaur Alasoo
2 days later
I gather that this is resolved? If not please provide full sessionInfo after the error is triggered.
On Mon, Oct 13, 2025 at 9:56?AM Kaur Alasoo <kauralasoo at gmail.com> wrote:
Hello, I am the maintainer of the wiggleplotr package and I have an error in the vignette that I cannot seem to figure out. When I look at the build report ( https://bioconductor.org/checkResults/devel/bioc-LATEST/wiggleplotr/nebbiolo2-buildsrc.html) I see the following error: Quitting from wiggleplotr.Rmd:65-67 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `plotTranscripts()`: ! object 'ccds' not found --- Backtrace: ? 1. ??wiggleplotr::plotTranscripts(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I can reproduce this error when I run R CMD build on my computer. However, when I try to debug the code interactively in R then everything works fine. I've not made any changes to the code or the package data outside the vignette. Is there something obvious that I am missing? Best, Kaur [[alternative HTML version deleted]]
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3 days later
Yes, I managed to solve it now. It was a bug introduced four years ago that now broke the build, but it might have been that when I fixed another bug I pushed the old bug into the bioconductor repository (perhaps it was previously in my own github only). This is why I got so confused. Best, Kaur On Mon, Oct 13, 2025 at 5:03?PM Vincent Carey <stvjc at channing.harvard.edu> wrote:
I gather that this is resolved? If not please provide full sessionInfo after the error is triggered. On Mon, Oct 13, 2025 at 9:56?AM Kaur Alasoo <kauralasoo at gmail.com> wrote:
Hello, I am the maintainer of the wiggleplotr package and I have an error in the vignette that I cannot seem to figure out. When I look at the build report (
I see the following error: Quitting from wiggleplotr.Rmd:65-67 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `plotTranscripts()`:
! object 'ccds' not found
---
Backtrace:
?
1. ??wiggleplotr::plotTranscripts(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I can reproduce this error when I run R CMD build on my computer.
However,
when I try to debug the code interactively in R then everything works
fine.
I've not made any changes to the code or the package data outside the
vignette.
Is there something obvious that I am missing?
Best,
Kaur
[[alternative HTML version deleted]]
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