get_bcc: use bco2df to acquire limited data frames from BiocCheck...

In vjcitn/BiocBuildTools: Bioconductor software ecosystem building tools

use bco2df to acquire limited data frames from BiocCheck applied to packages

Description

use bco2df to acquire limited data frames from BiocCheck applied to packages

Usage

get_bcc(
  sources.folder,
  bcchecks.destination,
  bcobj.destination,
  BPPARAM = bpparam(),
  BPOPTIONS = bpoptions()
)

Arguments

sources.folder	character(1) path to github checkouts of Bioc packages
bcchecks.destination	character(1) path to a writeable folder where BiocCheck logs are written
bcobj.destination	character(1) path to a folder where RDS files with data frames are written
BPPARAM	defaults to bpparam()
BPOPTIONS	defaults to bpoptions()

Examples

ps = PackageSet("parody")
tf = tempfile()
td = dir.create(tf)
populate_local_gits(ps, tf)
dir.create(bcdest <- tempfile("bcd"))
dir.create(bcodest <- tempfile("bco"))
get_bcc(tf, bcdest, bcodest)
readRDS(dir(bcodest, full=TRUE))
## Not run: 
set.seed(1234) # we shuffle packages to avoid restarting on a bad one
bcchecks.destination = dir.create(tempfile("bccheck"))
bcobj.destination = dir.create(tempfile("bcobj"))
spar = BiocParallel::SnowParam(3, threshold="DEBUG")
BiocParallel::bplog(spar) = TRUE
# make 777 BiocParallel::bplogdir(spar) = "~/BBS_space/BPLOGS_bc"
BiocParallel::bptimeout(spar) = 600
BiocParallel::register(spar)
# get_bcc(  ...

## End(Not run)

vjcitn/BiocBuildTools documentation built on March 15, 2024, 4:19 a.m.