getPackageTitles: Retrieve list of package titles and print package Description
In Bioconductor/biocViews: Categorized views of R package repositories

getPackageTitles

R Documentation

Retrieve list of package titles and print package Description

Description

These functions visit two Bioconductor releases branches, identifying differnt packages that are present in the ‘current’ repository from the ‘previous’ release. Utilizes the devel branch of bioconductor to retrieve description.

Usage

getPackageTitles(prevBranch="RELEASE_3_6",
                 currBranch="devel",
                 manifest=c("software.txt", "data-experiment.txt", 
                   "workflows.txt", "data-annotation.txt", "books.txt"),
                 status = c("new", "removed"))
getPackageDescriptions(pkgs, outfile, output=c("md", "text"), relativeLink=FALSE)

Arguments

`prevBranch`	`character(1)` Bioconductor branch to compare to
`currBranch`	`character(1)` Bioconductor branch for current packages.
`manifest`	`character(1)` Which repository of pakcages to compare. software.txt is software packages, data-experiment.txt is for data experiment packages and workflows.txt for workflow packages
`status`	get new or removed package list comparing currBranch to prevBranch
`pkgs`	character() A list of packages to retrieve DESCRIPTION
`outfile`	`character(1)` file path to the location where DESCRIPTIONS will be printed.
`output`	`character(1)` output to text or markdown format.
`relativeLink`	Should links to packages be relative links on bioconductor.org website or include full url 'https//bioconductor.org'. default: FALSE is full url.

Value

A list of package titles.

Author(s)

Martin Morgan mtmorgan@fhcrc.org and Lori Shepherd

Examples

## Not run: 
# At release time get a list of new or removed or deprecated packages

# get new packages in release 3.7 that are not in 3.6
newSoft = getPackageTitles()
# get removed packages from 3.6 
rmSoft = getPackageTitles(currBranch="RELEASE_3_7", status="removed")
# get depreacted package for 3.7
deprecatedSoft = setdiff(getPackageTitles(status="removed"), rmSoft)

# repeated above for data-experiment packages
newData = getPackageTitles(manifest="data-experiment.txt")
rmData = getPackageTitles(currBranch="RELEASE_3_7", manifest="data-experiment.txt", status="removed")
deprecatedData = setdiff(getPackageTitles(manifest="data-experiment.txt", status="removed"), rmData)

## End(Not run)

Bioconductor/biocViews documentation built on Nov. 2, 2024, 7:23 a.m.