[Bioc-devel] Broken dependency (corncob) with new version of a package (detectseparation)

[Kern, Lori]

The Bioconductor builders will require using the updated versions of any package or system dependency so specifying a specific version in the description will not resolve on the Bioconductor builders.

If you do not have a set time frame for corncob making changes or if they even will, then removing corncob methods temporarily seems like an acceptable solution.

Cheers,


Lori Shepherd - 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 Matteo Calgaro <mcalgaro93 using gmail.com>
Sent: Monday, September 5, 2022 5:44 PM
To: bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: [Bioc-devel] Broken dependency (corncob) with new version of a package (detectseparation)

Hello,

I received a notification that my package "benchdamic" was failing to
build. The cause was the new version v0.3 of a CRAN package named
"detectseparation" which is a dependency of "corncob" which is a dependency
of "bencdamic".

So "corncob" stopped working as pointed out by this issue (
https://secure-web.cisco.com/1mASDAxup2PSPMhsFoCjbl9pQ1etbU8pLSwBOkr1pHzdo8b7pc7gG-y59KCVIeThVW6Gv4mtJ3nC2Qr-XZnyxMqqwGvQxPuubY_F4LO9TTdWLjXMNFmJf_iOhd-g2IELPvbJhEna3UeExXZUz66xqB1ZWaikyTXMP7PDzSkdGd5RhfsZraP07DuAMzNFIpruLjB4DoJ0QrkIrIe0rSNZtAvGJT7c110G8e4KKy4uIrDKOXXp6YQhb1sqdXCUYN5U-3SDPu2q354xD-qQ8o-FKUrYEHKBV_k7Ma1e1m2RKT3XskUdLMNVXyos9_90d6wyF/https%3A%2F%2Fgithub.com%2Fbryandmartin%2Fcorncob%2Fissues%2F141) and my package too. So
I made some changes at the description file of "benchdamic", including the
old version of "detectseparation" v0.2 among the "Depends" packages.

As locally I've installed the "detectseparation" v0.2 package, "benchdamic"
builds and installs correctly, however in the main and devel releases it
fails (all the packages are up-to-date there).

I think that a temporary solution could be removing "corncob" from the pool
of methods available in "benchdamic" until the maintainers solve the issue.
Do you see any other less invasive solution?

Thanks in advance,

Matteo Calgaro
PhD Student in Biotechnology
University of Verona

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