abichat/test.dep.bioc

test.dep.bioc

The goal of test.dep.bioc is to test installation of Bioconductor dependencies with GitHub Actions.

Installation

remotes::install_github("abichat/test.dep.bioc")

Configurations tested

With limma (no recursive bioconductor dependencies)

No Remotes field

• Pass GitHub Actions.

• Can’t be installed with install_github():

dependency ‘limma’ is not available for package ‘test.dep.bioc’

Remotes with bioc::release/limma style

• GitHub Action failed:

Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: ! pkgdepends resolution error for deps::..
  Caused by error: 
  ! Cannot determine package name for 1 package: "bioc::release/limma".
  ℹ Maybe you need to add a `<packagename>=` prefix?

• Can be installed with install_github().

Remotes with bioc::limma style

• Pass GitHub Actions.

• Can be installed with install_github().

With affy (recursive bioconductor dependency on Biobase)

No Remotes field

• Pass GitHub Actions.

• Can’t be installed with install_github():

dependencies ‘affy’, ‘limma’ are not available for package ‘test.dep.bioc’

Remotes with bioc::release/limma style

• GitHub Action failed:

Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: ! pkgdepends resolution error for deps::..
  Caused by error: 
  ! Cannot determine package names for 2 packages: "bioc::release/affy" and
  "bioc::release/limma".
  ℹ Maybe you need to add a `<packagename>=` prefix?

• Can be installed with install_github().

Remotes with bioc::limma style

• Pass GitHub Actions.

• Can be installed with install_github().

With affy (recursive bioconductor dependency on Biobase) and Biobase

All Bioconductor Imports in Remotes with bioc::limma style

Remotes:
    bioc::affy,
    bioc::Biobase,
    bioc::limma

• GitHub Action failed:

Error: 
  ! error in pak subprocess
  Caused by error: 
  ! Could not solve package dependencies:
  * deps::.: Can't install dependency bioc::affy
  * bioc::affy: Can't install dependency Biobase (>= 2.5.5)

• Can be installed with install_github().

Only “terminal Imports Bioconductor dependencies” in Remotes with bioc::limma style

Remotes:
    bioc::affy,
    bioc::limma

• Pass GitHub Actions.

• Can be installed with install_github().