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Tools to deal with dependencies in scripts, Rmd and packages
https://thinkr-open.github.io/attachment/
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Deal with Bioconductor dependencies in find_remotes() #40

Closed statnmap closed 2 years ago

statnmap commented 2 years ago

For now in extract_pkg_info(),

Check that this is correct.

What is desired (for examples) ?

DESCRIPTION

Imports:
    SummarizedExperiment
Remotes:
  bioc::3.3/SummarizedExperiment#117513, bioc::release/Biobase
statnmap commented 2 years ago

What about filling DESCRIPTION with the correct Bioconductor field ?

# Test bioconductor ?
attachment::find_remotes(installed.packages()[,1])
BiocManager::install("XVector")
packageDescription("XVector")
BiocManager::valid("XVector")
debugonce(extract_pkg_info)
find_remotes("BiocVersion")
MurielleDelmotte commented 2 years ago 
find_remotes("BiocVersion")
$BiocVersion
local maybe ? 
           NA

car: 

> packageDescription("XVector")$RemoteType
NULL

> packageDescription("XVector")$RemoteURL
NULL

> packageDescription("XVector")$RemoteHOST
NULL
statnmap commented 2 years ago

It seems that all these writing are valid: 

if (FALSE) {
install_bioc("SummarizedExperiment")
install_bioc("devel/SummarizedExperiment")
install_bioc("3.3/SummarizedExperiment")
install_bioc("SummarizedExperiment#abc123")
install_bioc("user:password@release/SummarizedExperiment")
install_bioc("user:password@devel/SummarizedExperiment")
install_bioc("user:password@SummarizedExperiment#abc123")
}

Let's focus only on the simplest one: install_bioc("SummarizedExperiment") or install_bioc("3.3/SummarizedExperiment")

statnmap commented 2 years ago

Added in https://github.com/ThinkR-open/attachment/pull/61