In vjcitn/BiocBuildTools: Bioconductor software ecosystem building tools

title: "Components of ecosystem assessment with BiocBuildTools" author: "Vincent J. Carey, stvjc at channing.harvard.edu" date: "r format(Sys.time(), '%B %d, %Y')" vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{Components of ecosystem assessment with BiocBuildTools} %\VignetteEncoding{UTF-8} output: BiocStyle::html_document: highlight: pygments number_sections: yes theme: united toc: yes

suppressMessages({
suppressPackageStartupMessages({
library(BiocStyle)
library(BiocBuildTools)
library(BiocPkgTools)
library(igraph)
library(dplyr)
library(magrittr)
})
})

Overview

In this vignette we illustrate the use of software to capture information from R CMD check and BiocCheck::BiocCheck in concise formats.

Harvesting check outputs

Acquire some source repos

td = tempdir()
od = getwd()
setwd(td)
library(BiocBuildTools)
ps = PackageSet(c("parody", "BiocFileCache"))
getwd()
system("mkdir gits")
populate_local_gits(ps, "gits")

Some helper software

date_string = function(x) as.character(as.Date(x, origin="1970-01-01"))
last_commit_date = function(repo) {
  ans = Sys.time() + NA # if gert not available, produce a classed NA
  if (requireNamespace("gert")) ans = gert::git_log(repo=repo, max=1)$time
  ans
}

Run R CMD check

setwd(td)
rc = lapply(dir("gits", full=TRUE), function(x) {
   ans = rcmdcheck::rcmdcheck(x,quiet=TRUE)
   attr(ans, "last_commit_date") <- last_commit_date(x)
   attr(ans, "check_date") <- Sys.time()
   attr(ans, "pkgversion") <- ans$version
   ans
   })
rdfs = rcclist_to_dataframes(rc)

Run BiocCheck

In this chunk we use BiocParallel to get separate processes for BiocCheck runs. Without this we can see namespace detachment problems.

setwd(td)
library(BiocParallel)
register(SnowParam(2))  # gets around namespace detachment issue
ini = dir("gits")
bdfs = bplapply(dir("gits", full=TRUE), function(x) {
   ans = BiocCheck::BiocCheck(x)
   attr(ans, "last_commit_date") <- last_commit_date(x)
   attr(ans, "check_date") <- Sys.time()
   attr(ans, "pkgversion") <- ans$metadata$PackageVersion
   bco2df(ans)
   })
names(bdfs) = ini