[Bioc-devel] knitr ERROR on Biocondcutor builders

[Kern, Lori]

Developers,

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 (BBS-noreply using bioconductor.org) 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.

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263


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