In vjcitn/bbsBuildArtifacts: analyze build artifacts for Bioconductor

Identifying packages with new events relative to a prior build

We have introduced new_events and becomes_OK functions to help assess differences in package state over time.

To use this, we need multiple ArtifSet instances. This is time-consuming so we just record a past application:

> rel_911 = setup_artifacts(date="2022-09-11", version="3.15")
starting untar...
done.

> rel_916 = setup_artifacts(date="2022-09-16", version="3.15")
starting untar...
done.

We indicate the type of event and the host name to get a report on which packages have been revised to eliminate all errors between 9-11 and 9-16.

> becomes_OK(rel_911, rel_916, event="ERROR", host="nebbiolo1")
[1] "GSVA"        "NetSAM"      "netZooR"     "OrganismDbi" "PPInfer"    
[6] "pRoloc"      "TFHAZ"      

Here are some additional examples:

> new_events(rel_911, rel_916, event="ERROR", host="nebbiolo1")
[1] "BEclear"      "imageHTS"     "iPAC"         "martini"      "singleCellTK"

> new_events(rel_911, rel_916, event="ERROR", host="palomino3")
[1] "BEclear"      "martini"      "NuPoP"        "SCANVIS"      "singleCellTK"
[6] "Travel"      

> new_events(rel_911, rel_916, event="WARNINGS", host="palomino3")
[1] "edge"  "normr" "ORFik"

Comparing package states across platforms

The idiosync_status function will report on packages that exhibit events of specific types on only a subset of platforms in use.

> af = setup_artifacts()
trying URL 'https://bioconductor.org/checkResults/3.15/bioc-LATEST/report.tgz'
Content type 'application/x-gzip' length 52390769 bytes (50.0 MB)
==================================================
downloaded 50.0 MB

starting untar...
done.
> idiosync_status(af)
$linux_only
[1] "HTSeqGenie" "iPAC"      

$win_only
 [1] "affyPLM"      "BiocParallel" "FlowSOM"      "GRridge"      "IgGeneUsage" 
 [6] "Macarron"     "motifcounter" "NetSAM"       "NuPoP"        "OmnipathR"   
[11] "oneSENSE"     "RGMQL"        "rtracklayer"  "SCANVIS"      "Travel"      
[16] "waddR"       

$mac_only
[1] "biodbMirbase" "netZooR"     

> idiosync_status(af, phase="install")
$linux_only
character(0)

$win_only
[1] "CONFESS"    "ddPCRclust" "flowPeaks"  "rifi"      

$mac_only
character(0)

vjcitn/bbsBuildArtifacts documentation built on Aug. 6, 2023, 2:06 p.m.