Package: BiocPkgTools 1.31.14

Sean Davis

BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.

Authors:Shian Su [aut, ctb], Lori Shepherd [ctb], Marcel Ramos [aut, ctb], Felix G.M. Ernst [ctb], Jennifer Wokaty [ctb], Charlotte Soneson [ctb], Martin Morgan [ctb], Vince Carey [ctb], Sean Davis [aut, cre]

BiocPkgTools_1.31.14.tar.gz
BiocPkgTools_1.31.14.zip(r-4.7)BiocPkgTools_1.31.14.zip(r-4.6)BiocPkgTools_1.31.14.zip(r-4.5)
BiocPkgTools_1.31.14.tgz(r-4.6-any)BiocPkgTools_1.31.14.tgz(r-4.5-any)
BiocPkgTools_1.31.14.tar.gz(r-4.7-any)BiocPkgTools_1.31.14.tar.gz(r-4.6-any)
BiocPkgTools_1.31.14.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiocPkgTools/json (API)

# Install 'BiocPkgTools' in R:

install.packages('BiocPkgTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/seandavi/biocpkgtools/issues

On BioConductor:BiocPkgTools-1.31.12(bioc 3.24)BiocPkgTools-1.30.1(bioc 3.23)

software infrastructure bioconductor metadata u24ca289073

8.94 score 22 stars 1 packages 126 scripts 638 downloads 1 mentions 48 exports 92 dependencies

Last updated from:ceae38a1bb. Checks:1 WARNING, 4 ERROR, 2 OK, 3 NOTE. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	158
linux-devel-x86_64	ERROR	482
source / vignettes	OK	303
linux-release-x86_64	ERROR	491
macos-release-arm64	NOTE	394
macos-oldrel-arm64	ERROR	395
windows-devel	NOTE	888
windows-release	NOTE	1005
windows-oldrel	ERROR	892
wasm-release	OK	161

Exports:activitySince anacondaDownloadStats biocBuildEmail biocBuildReport biocBuildReportDB biocBuildStatusDB biocDownloadStats biocExplore biocMaintained biocPkgList biocPkgRanges biocRevDepEmail biocVIEWSdb buildClassDepData buildClassDepFromPackage buildClassDepGraph buildPkgDependencyDataFrame buildPkgDependencyIgraph CRANstatus firstInBioc get_bioc_data get_cre_orcids getBiocVignette getPackageInfo getPkgYearsInBioc githubDetails githubURLParts hasBiocMaint inducedSubgraphByPkgs latestPkgStats orcid_table pkgBiocDeps pkgBiocRevDeps pkgCombDependencyGain pkgDepImports pkgDepMetrics pkgDownloadRank pkgDownloadStats pkgToolsCache plotClassDep plotClassDepData plotClassDepGraph problemPage repositoryStats sentHistory setCache subgraphByDegree templatePath

Dependencies:askpass base64enc BH Biobase BiocFileCache BiocGenerics BiocManager biocViews bit bit64 bitops blob bslib cachem cli clipr cpp11 crayon crosstalk curl DBI dbplyr digest dplyr DT evaluate fastmap filelock fontawesome fs generics gitcreds glue graph highr hms htmltools htmlwidgets httr httr2 igraph ini jquerylib jsonlite knitr later lattice lazyeval lifecycle lubridate magrittr Matrix memoise mime openssl otel pillar pkgconfig prettyunits progress promises purrr R6 rappdirs RBGL Rcpp RCurl readr rlang rmarkdown RSQLite RUnit rvest sass selectr stringi stringr sys tibble tidyr tidyselect timechange tinytex tzdb utf8 vctrs vroom withr xfun XML xml2 yaml

Overview of BiocPkgTools

Rendered fromBiocPkgTools.Rmdusingknitr::rmarkdown

Last update: 2026-06-26
Started: 2017-12-08

Help page	Topics
get the ORCID id from cre field of Authors@R in packageDescription result	.get_cre_orcid
What are the issues, pulls, commits created since a date?	activitySince
Get download statistics for Bioconductor packages distributed via Anaconda.	anacondaDownloadStats
Create and copy e-mail package notification template to clipboard	biocBuildEmail sentHistory
Tidy Bioconductor build report results	biocBuildReport
Parse the Build Report tarball for a Bioconductor release	biocBuildReportDB
Download and parse the build status information for Bioconductor packages	biocBuildStatusDB
Get Bioconductor download statistics	biocDownloadStats
Explore Bioconductor packages interactively	biocExplore
Bioconductor Maintained Packages	biocMaintained hasBiocMaint
Get full Bioconductor software package listing, with details	biocPkgList
Grab build report results from BUILD_STATUS_DB for a particular package range	biocPkgRanges
BiocPkgTools: Examine and analyze Bioconductor package metadata	BiocPkgTools-package BiocPkgTools
Manage cache for BiocPkgTools	BiocPkgTools-cache pkgToolsCache setCache
Notify downstream maintainers of changes in upstream packages	biocRevDepEmail
Parse and return the VIEWS file for a Bioconductor Release	biocVIEWSdb
Work with Bioconductor package dependencies	buildPkgDependencyDataFrame
Work with package dependencies as a graph	buildPkgDependencyIgraph
Retrieve Class relationships	buildClassDepData buildClassDepFromPackage buildClassDepGraph class-dependencies plotClassDep plotClassDepData plotClassDepGraph
Check the CRAN build report page and email a notification	CRANstatus
When did a package enter Bioconductor?	firstInBioc
Generate a DOI for a Bioconductor package	generateBiocPkgDOI
Get data from Bioconductor	get_bioc_data
get ORCID ids from cre fields of Authors@R in packageDescription results	get_cre_orcids
Download a Bioconductor vignette	getBiocVignette
Generate needed information to create DOI from a package directory.	getPackageInfo
Calculate the years in Bioconductor	getPkgYearsInBioc
Get package details from GitHub	githubDetails
Extract GitHub user and repo name from GitHub URL	githubURLParts
Return a minimal subgraph based on package name(s)	inducedSubgraphByPkgs
Summary of the latest package statistics	latestPkgStats
Obtain employment data from ORCID	orcid_table
Look up a package's Bioconductor dependencies	pkgBiocDeps
Obtain all the reverse dependencies for a Bioconductor package	pkgBiocRevDeps summary.biocrevdeps
Calculate dependency gain achieved by excluding combinations of packages	pkgCombDependencyGain
Report package imported functionality	pkgDepImports
Report package dependency burden	pkgDepMetrics
What is a package's download rank?	pkgDownloadRank
Get Bioconductor download statistics for a package	pkgDownloadStats
generate hyperlinked HTML for build reports for Bioc packages	problemPage
Bioconductor Binary Repository Statistics	print.repositoryStats repositoryStats
Subset graph by degree	subgraphByDegree
Obtain the location of available email templates	templatePath

Package: BiocPkgTools 1.31.14

BiocPkgTools: Collection of simple tools for learning about Bioconductor Packages

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Usage by other packages (reverse dependencies)