[Bioc-devel] Error in trio package due to removed package

[Kern, Lori]

We will not allow github only packages.  This is strictly against Bioconductor policy. All dependencies must be actively maintained on CRAN or Bioconductor.

Your package will not be deprecated given the short time frame and you will be able to consider options and fix the package over the next release time period as it will still show (albeit ERRORing/Broken) in release and devel. Just ensure any fix then is applied to both the release branch and devel branch of Bioconductor

Cheers,


Lori Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Holger Schwender via Bioc-devel <bioc-devel using r-project.org>
Sent: Wednesday, April 1, 2026 8:54 AM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Error in trio package due to removed package

Dear Bioconductor team,

I've just got a notification that checking/building my BioC package trio fails. The reason for the error is that a function in trio depends on a function from the package haplo.stats that was very recently removed from CRAN

https://secure-web.cisco.com/1JR0KTOD7ZXmI5eG6pR2F9wwSh3b1VnDZtdKmkNZn1gifHhlTzVI6yNgUu4S3VXM1t6NhvfcExibNPip0eI_uBiV39cUXvxSPJz3TC-2otuFIxac0MeuhJ1rddVwRa5neMeDkTwCfjejOjISU_GyNxCI529MkW7RInE1hK_YGztpTFmRW2HNhPCsUaDnKiXaArLIzUam9i-H2t4ufbqNOWYmcTgs8so69vvR95mgvJppiR4F8CnuoxWUR2QErWqMFHG3_rMHI8Gio80Lc4qxRyOyBU5Ct6Di_pr_8J0t7sz8_mC_J8xP33lOuIJFmLYHy/https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fhaplo.stats%2Findex.html

Rewriting the function in trio so that it would not depend on the haplo.stats function would be hardly possible, in particular considering the BioConductor release schedule. Even though this function is not one of the main features of the trio package, it is part of a workflow. So simply removing (temporarily) this function would also be not that simple (and not a really good idea).

The haplo.stats package, however, is still available at github (and the function used from this package does not seem to cause the problem because of which haplo.stats was removed from CRAN).

I would therefore be very grateful if you would let me know if it would be possible to also use a package that is only available at github as Suggest or Import in a BioConductor package, and if yes, if it would be okay to do so for the next release (and to remove this dependency until the release in October/November).

Thanks a lot,
Holger

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