UCSCRepeatMasker

[rcastelo]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/functionalgenomics/UCSCRepeatMasker

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[bioc-issue-bot]

Dear @rcastelo,

The package version number, '3.15.2', is not formatted correctly. Expecting format: 'x.99.z'.

Please fix your version number. See Bioconductor version numbers Please also remember to run BiocCheck::BiocCheck('new-package'=TRUE) on your package before submitting a new issue. BiocCheck will look for other Bioconductor package requirements.

[lshep]

I realize this is an exception because of how we do annotation packages

[bioc-issue-bot]

Dear @rcastelo ,

We have reopened the issue to continue the review process. Please remember to push a version bump to git.bioconductor.org to trigger a new build.

[lshep]

@rcastelo When I am trying to build and check on my local computer I am having trouble with the download concerning the SSL certificate of where you are hosting the data.

> ah[["AH99003"]]
downloading 1 resources
retrieving 1 resource
Error: failed to load resource
  name: AH99003
  title: UCSC RepeatMasker annotations (Sep2021) for Human (hg38)
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/105749'
  local file path: '/home/shepherd/.cache/R/AnnotationHub/2b7e1709f0a1_105749'
  reason: SSL certificate problem: unable to get local issuer certificate 
2: bfcadd() failed; resource removed
  rid: BFC23
  fpath: 'https://annotationhub.bioconductor.org/fetch/105749'
  reason: download failed 
3: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/105749'
  cache resource: 'AH99003 : 105749'
  reason: bfcadd() failed; see warnings() 

I tested several other resources hosted on the Bioconductor Azure server, direct access from ensembl, as well as others and don't run into this error so I can only assume it is an issue with https://functionalgenomics.upf.edu/annotationhub/repeatmasker/ please investigate

[rcastelo]

You're right, this was working smoothly on my Linux workstation, where the package and the vignette (which includes an actual example of downloading one such resources) build without errors and warning, but I can get also that error from my laptop (macOS 10.15.7) connected to the same network as my workstation. It seems that our IT department renewed the HTTPS certificate of our server on January and since this was working fine before with other AnnotationHub resources, my guess is that something changed after that renewal. I've already contacted them and hope that they can fix it soon. I'll keep you posted on this channel.

[rcastelo]

Hi @lshep the problem has been sorted out. Our IT department changed the certificate authority in the last renewal of our server's SSL certificate on January, and while in principle we had updated it, the intermediate CA in our server was still pointing out to the old authority. Now you should be able to build and check in your local computer without any issue, or at least, without that specific issue.

[lshep]

Manually Added. This had to be processed differently because it was an annotation package. It was added to manifest and on git and should propagate by the end of the week. If it does not please let us know and we will look into the issue.