The final list of deprecated packages for Bioc 3.9 is as follows:

Maintainer requested deprecation:

• Software:

  • flowQ
  • miRsponge (renamed to miRspongeR)

Unresponsive/not-maintained packages:

• Software:

  • ProCoNA
  • GOTHic
  • htSeqTools
  • rMAT
  • TSSi
  • gCrisprTools

• Experiment Data Package:

  • PGPC

As the release deadlines approach, we will be sending emails out to packages that are broken across any platform in Bioconductor. We appreciate your timely response in fixing packages. Any package that has been warned, and is failing across ALL platforms will be up for immediate deprecation in devel 3.10. Thank you

There are two other software package that will be deprecated for this coming release.

NGScopy
spliceSites

gCrisprTools has reached out and the package will no longer be deprecated.

flowQB and flowQBData will be deprecated.

DOQTL has also requested deprecation.

GOTHiC has been undeprecated