new_config may not exist at end of zzz.R

[vjcitn]

Error: package or namespace load failed for ‘VariantAnnotation’: .onLoad failed in loadNamespace() for 'biomaRt', details: call: httr::set_config(new_config, override = FALSE) error: object 'new_config' not found Error : package ‘VariantAnnotation’ could not be loaded Error: loading failed Execution halted

not easy to reproduce, but popped up in https://github.com/vjcitn/gwaslake/runs/1753964971?check_suite_focus=true

i think early initialization of new_config to the most likely successful value will beat this

[grimbough]

Hi Vince,

Thanks for the report. I'm already working through this in #39. I think it is somewhat GitHub specific as I haven't seen it anywhere else. I'm particularly baffled as to why the biomaRt's own R CMD check workflow action seems to work fine.

I've got a branch that probably still fails, but should print more diagnostics of the problem.

BiocManager::install('grimbough/biomaRt', ref = '3_12_testing')

It'd be awesome if you could install that version explicitly in a workflow and then point me to the output.

[vjcitn]

I will try to do this later.

On Sat, Jan 23, 2021 at 8:43 AM Mike Smith notifications@github.com wrote:

Hi Vince,

Thanks for the report. I'm already working through this in #39 https://github.com/grimbough/biomaRt/issues/39. I think it is somewhat GitHub specific as I haven't seen it anywhere else. I'm particularly baffled as to why the biomaRt's own R CMD check workflow action seems to work fine.

I've got a branch that probably still fails, but should print more diagnostics of the problem.

BiocManager::install('grimbough/biomaRt', ref = '3_12_testing')

It'd be awesome if you could install that version explicitly in a workflow and then point me to the output.

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[vjcitn]

I used your 3_12_testing ref and had no problem. Thanks, can close if you like!

[NathanSkene]

Hi, we're getting the same issue occurring during Travis build checks for the EWCE package. Can't understand from above messages what you did to resolve this? Thanks

[vjcitn]

Can you force travis to use the biocmaRt imsage that gets installed via BiocManager::install('grimbough/biomaRt', ref = '3_12_testing')? Perhaps by using a Remotes: setting in DESCRIPTION?

[grimbough]

This should already be resolved in the sense that the fix has been pushed to the release branch of Bioconductor, but you'll need to wait for it to propagate through the build system. I pushed it a few day ago, so I'm surprised it hasn't made it yet, but when http://bioconductor.org/checkResults/release/bioc-LATEST/biomaRt/ ticks over to version 2.46.2 the issue should go away.

If you really need it now then it should be sufficient to install with:

BiocManager::install('grimbough/biomaRt', ref = 'RELEASE_3_12')

[grimbough]

It looks like 2.46.2 is now the version available from Bioconductor release. Hopefully that's the problem resolved. Please re-open this issue if you still experience the package failures.