Please be advised: There are still 152 packages currently showing ERROR on the Bioconductor devel build report because of the updates to knitr requiring a simple fix to the package DESCRIPTION. We reported that this is a real ERROR that needs to be corrected in all packages by the package maintainers.
See this post from June: https://stat.ethz.ch/pipermail/bioc-devel/2021-June/018223.html
Packages that are not fixed in the next month will be marked as deprecated until corrected. Packages that remained deprecated through the next Bioconductor release will be removed.
As of today Monday June 26 here is a list of packages that have this type of ERROR. These package maintainers should have been receiving the automatic build failure notifications from the BBS (BBSemail@example.com) and within the next few days will get a reminder email from the core team as well. We encourage if you know any of the package maintainers in this list to reach out to them to fix their package as soon as possible.
ABAEnrichment ADAM ADAMgui alpine ANCOMBC ASAFE AWFisher ballgown BiFET biobroom BiocSklearn BioMM BrainSABER ChIPanalyser CHRONOS CINdex clonotypeR cmapR COMPASS ComPrAn CopyNumberPlots CoRegNet corral CountClust CSSQ CytoDx deco DEComplexDisease DeMixT diffUTR distinct divergence DMCHMM EMDomics EnMCB epivizr epivizrChart fcoex flowCut flowDensity flowViz fmrs gCrisprTools GSCRNATools gEM GeomxTools getDEE2 GISPA globalSeq GofuncR gscreend h5vc HDTD hiAnnotator hiReadsProcessor hmbdQuery HPAStainR interactiveDisplayBase IntEREst IPO IRISFGM isomiRs iteremoval ivygapSE karyoploteR KEGGlincs ldblock levi LineagePulse Maaslin2 MADSEQ MAGeCKFlute MBQN MDTS MEAT MetaCyto metavizr MetaVolcanoR MethPed miRLAB moanin MotifDb MPRAnalyze MSGFgui MSGFplus MsstatsQCgui multiClust NBSplice nearBynding netprioR netresponse nondetects NoRCE odseq openCyto oppti pandaR parglms pgca PICS pipeFrame plotGrouper pogos polyester pqsfinder proFIA profileScoreDist progeny ProteoMM psycenet2r qcmetrics QuaternaryProd Rbowtie2 rcellminer regioneR ReportingTools RepViz RlmmPort RIPAT RmassBank RNASeqR ROC RPA Rqc RTCGA RUVcorr SANTA scClassifR scds SCFA scHOT semisup SICtools sigFeature SISPA sitadela slalom SMITE ssrch strandCheckR SummarizedBenchmark Summix synlet TCGAbiolinksGUI tenXplore Tfutils topdownr trena VennDetail vsn XCIR zFPKM
Thank you. We appreciate everyone's contributions to Bioconductor and hope to have these ERRORs resolved quickly.