diff --git a/cran-comments.md b/cran-comments.md index 0644eba7e..5c3db95b3 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,24 +1,3 @@ ## revdepcheck results -We checked 7822 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 13 packages - -Issues with CRAN packages are summarised below. - -### Failed to check - -* bayesdfa (NA) -* Boom (NA) -* CausalImpact (NA) -* ctsem (NA) -* fdaPDE (NA) -* loon.ggplot (NA) -* loon.shiny (NA) -* loon.tourr (NA) -* Rborist (NA) -* rstanarm (NA) -* SSVS (NA) -* tidyfit (NA) -* vivid (NA) +We checked all reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. Unfortunately something is up with our revdep test system and I failed to check ~1200 packages. I'm pretty confident these are bioconductor packages and unrelated to changes to testthat. diff --git a/revdep/README.md b/revdep/README.md index a1c9ff597..0a52ce160 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,8 +1,1215 @@ # Revdeps +## Failed to check (1202) + +|package |version |error |warning |note | +|:------------------------------------------|:-------|:-----|:-------|:----| +|abseqR |? | | | | +|ADAM |? | | | | +|ADAMgui |? | | | | +|adductomicsR |? | | | | +|ADImpute |? | | | | +|aggregateBioVar |? | | | | +|airpart |? | | | | +|alabaster.base |? | | | | +|alabaster.bumpy |? | | | | +|alabaster.files |? | | | | +|alabaster.mae |? | | | | +|alabaster.matrix |? | | | | +|alabaster.ranges |? | | | | +|alabaster.sce |? | | | | +|alabaster.se |? | | | | +|alabaster.spatial |? | | | | +|alabaster.string |? | | | | +|alabaster.vcf |? | | | | +|ALDEx2 |? | | | | +|alevinQC |? | | | | +|AllelicImbalance |? | | | | +|AlpsNMR |? | | | | +|AMARETTO |? | | | | +|amplican |? | | | | +|ANCOMBC |? | | | | +|AneuFinder |? | | | | +|AnnotationFilter |? | | | | +|annotatr |? | | | | +|AnVIL |? | | | | +|AnVILBilling |? | | | | +|AnVILPublish |? | | | | +|APAlyzer |? | | | | +|apeglm |? | | | | +|APL |? | | | | +|artMS |? | | | | +|ASAFE |? | | | | +|ASICS |? | | | | +|ASSIGN |? | | | | +|ASURAT |? | | | | +|ATACseqQC |? | | | | +|ATACseqTFEA |? | | | | +|atSNP |? | | | | +|AUCell |? | | | | +|autonomics |? | | | | +|awst |? | | | | +|bacon |? | | | | +|ballgown |? | | | | +|bambu |? | | | | +|bamsignals |? | | | | +|BANDITS |? | | | | +|bandle |? | | | | +|banocc |? | | | | +|barcodetrackR |? | | | | +|basecallQC |? | | | | +|BASiCS |? | | | | +|BASiCStan |? | | | | +|basilisk |? | | | | +|basilisk.utils |? | | | | +|batchelor |? | | | | +|BatchQC |? | | | | +|bayesdfa |1.3.1 |1 | | | +|BayesSpace |? | | | | +|bayNorm |? | | | | +|beachmat |? | | | | +|beachmat.hdf5 |? | | | | +|BEARscc |? | | | | +|BEclear |? | | | | +|beer |? | | | | +|benchdamic |? | | | | +|benchmarkfdrData2019 |? | | | | +|BG2 |? | | | | +|BgeeCall |? | | | | +|BgeeDB |? | | | | +|BiFET |? | | | | +|BindingSiteFinder |? | | | | +|bioassayR |? | | | | +|biobroom |? | | | | +|biobtreeR |? | | | | +|bioCancer |? | | | | +|BioCartaImage |? | | | | +|BiocBook |? | | | | +|BiocFHIR |? | | | | +|BiocFileCache |? | | | | +|BiocHail |? | | | | +|BiocIO |? | | | | +|BiocNeighbors |? | | | | +|BiocOncoTK |? | | | | +|BioCor |? | | | | +|BiocPkgTools |? | | | | +|BiocSet |? | | | | +|BiocSingular |? | | | | +|BiocSklearn |? | | | | +|biocthis |? | | | | +|biodb |? | | | | +|biodbChebi |? | | | | +|biodbExpasy |? | | | | +|biodbHmdb |? | | | | +|biodbKegg |? | | | | +|biodbLipidmaps |? | | | | +|biodbMirbase |? | | | | +|biodbNcbi |? | | | | +|biodbNci |? | | | | +|biodbUniprot |? | | | | +|biomaRt |? | | | | +|BioMartGOGeneSets |? | | | | +|biomformat |? | | | | +|BioNAR |? | | | | +|BioNERO |? | | | | +|BioQC |? | | | | +|biosigner |? | | | | +|biotmle |? | | | | +|biscuiteer |? | | | | +|blacksheepr |? | | | | +|BloodGen3Module |? | | | | +|bluster |? | | | | +|BOBaFIT |? | | | | +|bodymapRat |? | | | | +|Boom |0.9.11 |1 | | | +|BP4RNAseq |? | | | | +|BPRMeth |? | | | | +|brainflowprobes |? | | | | +|breakpointR |? | | | | +|brendaDb |? | | | | +|BRGenomics |? | | | | +|BridgeDbR |? | | | | +|BSgenome.Hsapiens.UCSC.hg38.dbSNP151.major |? | | | | +|BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor |? | | | | +|BSgenomeForge |? | | | | +|bsseq |? | | | | +|bugsigdbr |? | | | | +|BUMHMM |? | | | | +|bumphunter |? | | | | +|BumpyMatrix |? | | | | +|BUSpaRse |? | | | | +|CaDrA |? | | | | +|cageminer |? | | | | +|canceR |? | | | | +|cardelino |? | | | | +|Cardinal |? | | | | +|CardinalIO |? | | | | +|CARNIVAL |? | | | | +|CATALYST |? | | | | +|CBEA |? | | | | +|cBioPortalData |? | | | | +|CBNplot |? | | | | +|cbpManager |? | | | | +|ccImpute |? | | | | +|ccmap |? | | | | +|CCPlotR |? | | | | +|celaref |? | | | | +|celda |? | | | | +|CellaRepertorium |? | | | | +|CellBarcode |? | | | | +|CellBench |? | | | | +|celldex |? | | | | +|CelliD |? | | | | +|cellity |? | | | | +|CellMixS |? | | | | +|CellScore |? | | | | +|cellxgenedp |? | | | | +|CEMiTool |? | | | | +|censcyt |? | | | | +|Cepo |? | | | | +|ceRNAnetsim |? | | | | +|CeTF |? | | | | +|cfDNAPro |? | | | | +|cfTools |? | | | | +|cfToolsData |? | | | | +|CHETAH |? | | | | +|Chicago |? | | | | +|chihaya |? | | | | +|chimeraviz |? | | | | +|chipenrich |? | | | | +|chipenrich.data |? | | | | +|ChIPexoQual |? | | | | +|ChIPpeakAnno |? | | | | +|ChIPseeker |? | | | | +|ChromSCape |? | | | | +|chromstaR |? | | | | +|chromVAR |? | | | | +|cicero |? | | | | +|CIMICE |? | | | | +|CINdex |? | | | | +|circRNAprofiler |? | | | | +|CircSeqAlignTk |? | | | | +|cleaver |? | | | | +|cliProfiler |? | | | | +|cliqueMS |? | | | | +|CluMSID |? | | | | +|clusterExperiment |? | | | | +|ClusterJudge |? | | | | +|clusterProfiler |? | | | | +|ClusterSignificance |? | | | | +|clustifyr |? | | | | +|ClustIRR |? | | | | +|cmapR |? | | | | +|CNEr |? | | | | +|CNVMetrics |? | | | | +|CNVPanelizer |? | | | | +|COCOA |? | | | | +|CoGAPS |? | | | | +|cogeqc |? | | | | +|Cogito |? | | | | +|cola |? | | | | +|comapr |? | | | | +|combi |? | | | | +|coMethDMR |? | | | | +|COMPASS |? | | | | +|compcodeR |? | | | | +|ComplexHeatmap |? | | | | +|CompoundDb |? | | | | +|ComPrAn |? | | | | +|compSPOT |? | | | | +|concordexR |? | | | | +|condiments |? | | | | +|consICA |? | | | | +|CopyNumberPlots |? | | | | +|coRdon |? | | | | +|CoreGx |? | | | | +|corral |? | | | | +|coseq |? | | | | +|CoSIA |? | | | | +|COSMIC.67 |? | | | | +|cosmosR |? | | | | +|COTAN |? | | | | +|countsimQC |? | | | | +|crisprBase |? | | | | +|crisprBowtie |? | | | | +|crisprBwa |? | | | | +|crisprDesign |? | | | | +|crisprScore |? | | | | +|crisprScoreData |? | | | | +|CRISPRseek |? | | | | +|CrispRVariants |? | | | | +|crisprVerse |? | | | | +|crisprViz |? | | | | +|crossmeta |? | | | | +|csaw |? | | | | +|csdR |? | | | | +|CTdata |? | | | | +|cTRAP |? | | | | +|ctsem |3.9.1 |1 | | | +|ctsGE |? | | | | +|CTSV |? | | | | +|curatedAdipoChIP |? | | | | +|curatedAdipoRNA |? | | | | +|CuratedAtlasQueryR |? | | | | +|curatedMetagenomicData |? | | | | +|curatedTBData |? | | | | +|curatedTCGAData |? | | | | +|customCMPdb |? | | | | +|cydar |? | | | | +|CyTOFpower |? | | | | +|cytofQC |? | | | | +|CytoGLMM |? | | | | +|cytoKernel |? | | | | +|cytomapper |? | | | | +|CytoML |? | | | | +|CytoPipeline |? | | | | +|CytoPipelineGUI |? | | | | +|cytoviewer |? | | | | +|dagLogo |? | | | | +|DAMEfinder |? | | | | +|DaMiRseq |? | | | | +|DAPAR |? | | | | +|dcanr |? | | | | +|DCATS |? | | | | +|dce |? | | | | +|ddCt |? | | | | +|dearseq |? | | | | +|debCAM |? | | | | +|debrowser |? | | | | +|decontX |? | | | | +|deconvR |? | | | | +|decoupleR |? | | | | +|DeepPINCS |? | | | | +|DEFormats |? | | | | +|DEGreport |? | | | | +|DelayedDataFrame |? | | | | +|DelayedMatrixStats |? | | | | +|DelayedRandomArray |? | | | | +|DelayedTensor |? | | | | +|demuxmix |? | | | | +|demuxSNP |? | | | | +|densvis |? | | | | +|DEP |? | | | | +|DepecheR |? | | | | +|DepInfeR |? | | | | +|derfinder |? | | | | +|derfinderHelper |? | | | | +|derfinderPlot |? | | | | +|DEScan2 |? | | | | +|DESeq2 |? | | | | +|DESpace |? | | | | +|destiny |? | | | | +|DEWSeq |? | | | | +|DEXSeq |? | | | | +|DIAlignR |? | | | | +|DiffBind |? | | | | +|diffcyt |? | | | | +|DifferentialRegulation |? | | | | +|diffHic |? | | | | +|DiffLogo |? | | | | +|diffuStats |? | | | | +|Dino |? | | | | +|dir.expiry |? | | | | +|discordant |? | | | | +|DiscoRhythm |? | | | | +|distinct |? | | | | +|dittoSeq |? | | | | +|DMCHMM |? | | | | +|DNABarcodeCompatibility |? | | | | +|DNAfusion |? | | | | +|DNAshapeR |? | | | | +|DNAZooData |? | | | | +|DominoEffect |? | | | | +|doppelgangR |? | | | | +|dorothea |? | | | | +|Doscheda |? | | | | +|DOSE |? | | | | +|doubletrouble |? | | | | +|drawProteins |? | | | | +|DRIMSeq |? | | | | +|DropletTestFiles |? | | | | +|DropletUtils |? | | | | +|dStruct |? | | | | +|Dune |? | | | | +|easier |? | | | | +|easierData |? | | | | +|easylift |? | | | | +|EBSeq |? | | | | +|EDASeq |? | | | | +|edge |? | | | | +|EDIRquery |? | | | | +|eds |? | | | | +|EGAD |? | | | | +|eisaR |? | | | | +|ELMER |? | | | | +|EmpiricalBrownsMethod |? | | | | +|emtdata |? | | | | +|enhancerHomologSearch |? | | | | +|EnMCB |? | | | | +|EnrichedHeatmap |? | | | | +|enrichTF |? | | | | +|enrichViewNet |? | | | | +|ensembldb |? | | | | +|EpiDISH |? | | | | +|epigraHMM |? | | | | +|epimutacions |? | | | | +|epistack |? | | | | +|epistasisGA |? | | | | +|EpiTxDb |? | | | | +|EpiTxDb.Hs.hg38 |? | | | | +|EpiTxDb.Mm.mm10 |? | | | | +|EpiTxDb.Sc.sacCer3 |? | | | | +|epivizr |? | | | | +|epivizrChart |? | | | | +|epivizrData |? | | | | +|epivizrServer |? | | | | +|epivizrStandalone |? | | | | +|esATAC |? | | | | +|escape |? | | | | +|EWCE |? | | | | +|ewceData |? | | | | +|ExperimentSubset |? | | | | +|ExploreModelMatrix |? | | | | +|ExpressionAtlas |? | | | | +|extraChIPs |? | | | | +|factR |? | | | | +|famat |? | | | | +|FastqCleaner |? | | | | +|fastreeR |? | | | | +|fdaPDE |1.1-16 |1 | | | +|FEAST |? | | | | +|FeatSeekR |? | | | | +|fedup |? | | | | +|FELLA |? | | | | +|fenr |? | | | | +|fgsea |? | | | | +|FindIT2 |? | | | | +|fishpond |? | | | | +|FLAMES |? | | | | +|flowAI |? | | | | +|flowClust |? | | | | +|flowCore |? | | | | +|flowGate |? | | | | +|flowGraph |? | | | | +|flowPloidy |? | | | | +|FlowSOM |? | | | | +|FlowSorted.Blood.EPIC |? | | | | +|FlowSorted.CordBloodCombined.450k |? | | | | +|flowSpecs |? | | | | +|flowStats |? | | | | +|flowViz |? | | | | +|flowWorkspace |? | | | | +|fmrs |? | | | | +|fobitools |? | | | | +|fourDNData |? | | | | +|FRASER |? | | | | +|frenchFISH |? | | | | +|GA4GHclient |? | | | | +|GA4GHshiny |? | | | | +|GARS |? | | | | +|gatom |? | | | | +|GBScleanR |? | | | | +|gcatest |? | | | | +|GDCRNATools |? | | | | +|gDR |? | | | | +|gDRcore |? | | | | +|gDRimport |? | | | | +|gDRstyle |? | | | | +|gDRtestData |? | | | | +|gDRutils |? | | | | +|GDSArray |? | | | | +|GEM |? | | | | +|gemini |? | | | | +|gemma.R |? | | | | +|geneAttribution |? | | | | +|geneClassifiers |? | | | | +|GENESIS |? | | | | +|GeneSummary |? | | | | +|GeneTonic |? | | | | +|geneXtendeR |? | | | | +|GENIE3 |? | | | | +|GenomAutomorphism |? | | | | +|GenomicDataCommons |? | | | | +|GenomicDistributions |? | | | | +|GenomicInteractionNodes |? | | | | +|GenomicInteractions |? | | | | +|GenomicPlot |? | | | | +|GenomicState |? | | | | +|GenomicSuperSignature |? | | | | +|GenomicTuples |? | | | | +|GenProSeq |? | | | | +|GenVisR |? | | | | +|GeoDiff |? | | | | +|GEOexplorer |? | | | | +|GEOfastq |? | | | | +|GeomxTools |? | | | | +|GEOquery |? | | | | +|GeoTcgaData |? | | | | +|gep2pep |? | | | | +|getDEE2 |? | | | | +|GeuvadisTranscriptExpr |? | | | | +|geva |? | | | | +|gg4way |? | | | | +|ggbio |? | | | | +|ggcyto |? | | | | +|ggkegg |? | | | | +|ggmanh |? | | | | +|ggmsa |? | | | | +|ggsc |? | | | | +|ggspavis |? | | | | +|ggtree |? | | | | +|ggtreeDendro |? | | | | +|ggtreeExtra |? | | | | +|GladiaTOX |? | | | | +|Glimma |? | | | | +|gllvm |1.4.3 |1 | | | +|glmGamPoi |? | | | | +|glmmrOptim |0.3.3 |1 | | | +|glmSparseNet |? | | | | +|globalSeq |? | | | | +|GloScope |? | | | | +|GmicR |? | | | | +|gmoviz |? | | | | +|GOfuncR |? | | | | +|GOpro |? | | | | +|GOSemSim |? | | | | +|goSTAG |? | | | | +|gpuMagic |? | | | | +|GRaNIE |? | | | | +|granulator |? | | | | +|graper |? | | | | +|graphite |? | | | | +|GSE159526 |? | | | | +|GSEABase |? | | | | +|GSEAmining |? | | | | +|GSgalgoR |? | | | | +|gtrellis |? | | | | +|GUIDEseq |? | | | | +|Gviz |? | | | | +|gwascat |? | | | | +|gwascatData |? | | | | +|GWENA |? | | | | +|HarmonizedTCGAData |? | | | | +|HarmonizR |? | | | | +|hca |? | | | | +|HCAData |? | | | | +|HCATonsilData |? | | | | +|HDO.db |? | | | | +|heatmaps |? | | | | +|hermes |? | | | | +|HERON |? | | | | +|Herper |? | | | | +|HGC |? | | | | +|hiAnnotator |? | | | | +|HiBED |? | | | | +|HiCcompare |? | | | | +|HiCDOC |? | | | | +|HiCExperiment |? | | | | +|HiContacts |? | | | | +|HiContactsData |? | | | | +|HiCool |? | | | | +|hicVennDiagram |? | | | | +|hierinf |? | | | | +|HilbertCurve |? | | | | +|HiLDA |? | | | | +|hipathia |? | | | | +|hiReadsProcessor |? | | | | +|hmdbQuery |? | | | | +|HMP16SData |? | | | | +|HMP2Data |? | | | | +|hoodscanR |? | | | | +|hpar |? | | | | +|HPO.db |? | | | | +|HTSFilter |? | | | | +|HubPub |? | | | | +|HumanTranscriptomeCompendium |? | | | | +|hypeR |? | | | | +|iasva |? | | | | +|icetea |? | | | | +|iCOBRA |? | | | | +|ideal |? | | | | +|idpr |? | | | | +|idr2d |? | | | | +|IgGeneUsage |? | | | | +|IHW |? | | | | +|IHWpaper |? | | | | +|imcdatasets |? | | | | +|imcRtools |? | | | | +|IMMAN |? | | | | +|ImmuneSpaceR |? | | | | +|immunoClust |? | | | | +|immunotation |? | | | | +|INDEED |? | | | | +|infercnv |? | | | | +|INTACT |? | | | | +|InTAD |? | | | | +|InteractionSet |? | | | | +|InteractiveComplexHeatmap |? | | | | +|InterCellar |? | | | | +|IntOMICS |? | | | | +|IntramiRExploreR |? | | | | +|IONiseR |? | | | | +|ipdDb |? | | | | +|ISAnalytics |? | | | | +|iSEE |? | | | | +|iSEEde |? | | | | +|iSEEhex |? | | | | +|iSEEhub |? | | | | +|iSEEindex |? | | | | +|iSEEpathways |? | | | | +|iSEEu |? | | | | +|IsoBayes |? | | | | +|IsoCorrectoR |? | | | | +|IsoCorrectoRGUI |? | | | | +|isomiRs |? | | | | +|ivygapSE |? | | | | +|karyoploteR |? | | | | +|katdetectr |? | | | | +|KBoost |? | | | | +|KEGGgraph |? | | | | +|LACE |? | | | | +|LedPred |? | | | | +|lefser |? | | | | +|lemur |? | | | | +|levi |? | | | | +|lfa |? | | | | +|lineagespot |? | | | | +|Linnorm |? | | | | +|lipidr |? | | | | +|LOLA |? | | | | +|LoomExperiment |? | | | | +|loon.shiny |? | | | | +|loon.tourr |? | | | | +|lpsymphony |? | | | | +|LRBaseDbi |? | | | | +|LRcell |? | | | | +|LRcellTypeMarkers |? | | | | +|m6Aboost |? | | | | +|Maaslin2 |? | | | | +|Macarron |? | | | | +|MACSQuantifyR |? | | | | +|MACSr |? | | | | +|magrene |? | | | | +|MAI |? | | | | +|mariner |? | | | | +|marinerData |? | | | | +|marr |? | | | | +|martini |? | | | | +|maser |? | | | | +|MAST |? | | | | +|mastR |? | | | | +|MatrixGenerics |? | | | | +|MatrixQCvis |? | | | | +|matter |? | | | | +|MBECS |? | | | | +|mbkmeans |? | | | | +|MCbiclust |? | | | | +|mdp |? | | | | +|MDTS |? | | | | +|MEAL |? | | | | +|MEAT |? | | | | +|megadepth |? | | | | +|Melissa |? | | | | +|memes |? | | | | +|MerfishData |? | | | | +|MeSHDbi |? | | | | +|metabCombiner |? | | | | +|metabinR |? | | | | +|MetaboAnnotation |? | | | | +|MetaboCoreUtils |? | | | | +|metabolomicsWorkbenchR |? | | | | +|metagenomeSeq |? | | | | +|MetaGxBreast |? | | | | +|MetaGxOvarian |? | | | | +|MetaGxPancreas |? | | | | +|MetaNeighbor |? | | | | +|metapod |? | | | | +|MetaScope |? | | | | +|MetCirc |? | | | | +|MethReg |? | | | | +|methrix |? | | | | +|methylCC |? | | | | +|methylGSA |? | | | | +|methylKit |? | | | | +|MethylMix |? | | | | +|MetNet |? | | | | +|mfa |? | | | | +|mgsa |? | | | | +|mia |? | | | | +|miaSim |? | | | | +|miaViz |? | | | | +|microbiome |? | | | | +|MicrobiomeBenchmarkData |? | | | | +|microbiomeDASim |? | | | | +|microbiomeDataSets |? | | | | +|microbiomeExplorer |? | | | | +|microbiomeMarker |? | | | | +|MicrobiomeProfiler |? | | | | +|MicrobiotaProcess |? | | | | +|microSTASIS |? | | | | +|MICSQTL |? | | | | +|midasHLA |? | | | | +|miloR |? | | | | +|mimager |? | | | | +|MIRA |? | | | | +|miRBaseVersions.db |? | | | | +|miRNAmeConverter |? | | | | +|miRNAtap |? | | | | +|missRows |? | | | | +|mistyR |? | | | | +|mitch |? | | | | +|mitoClone2 |? | | | | +|mixOmics |? | | | | +|MLInterfaces |? | | | | +|MLSeq |? | | | | +|MMUPHin |? | | | | +|moanin |? | | | | +|MobilityTransformR |? | | | | +|ModCon |? | | | | +|Modstrings |? | | | | +|MOFA2 |? | | | | +|MoleculeExperiment |? | | | | +|MOMA |? | | | | +|monaLisa |? | | | | +|monocle |? | | | | +|Moonlight2R |? | | | | +|MoonlightR |? | | | | +|mosbi |? | | | | +|MOSim |? | | | | +|motifcounter |? | | | | +|motifmatchr |? | | | | +|MouseFM |? | | | | +|MPO.db |? | | | | +|MQmetrics |? | | | | +|MSA2dist |? | | | | +|MsBackendMassbank |? | | | | +|MsBackendMgf |? | | | | +|MsBackendMsp |? | | | | +|MsBackendRawFileReader |? | | | | +|MsBackendSql |? | | | | +|MsCoreUtils |? | | | | +|MsDataHub |? | | | | +|MsExperiment |? | | | | +|MsFeatures |? | | | | +|msigdb |? | | | | +|MSnbase |? | | | | +|MSPrep |? | | | | +|msPurity |? | | | | +|msqc1 |? | | | | +|msqrob2 |? | | | | +|MsQuality |? | | | | +|MSstatsQC |? | | | | +|MSstatsShiny |? | | | | +|MSstatsTMT |? | | | | +|MuData |? | | | | +|MultiAssayExperiment |? | | | | +|multicrispr |? | | | | +|MultiDataSet |? | | | | +|multiGSEA |? | | | | +|multiHiCcompare |? | | | | +|multiMiR |? | | | | +|MultiRNAflow |? | | | | +|multiWGCNA |? | | | | +|mumosa |? | | | | +|MungeSumstats |? | | | | +|muscat |? | | | | +|musicatk |? | | | | +|MutationalPatterns |? | | | | +|mzID |? | | | | +|NADfinder |? | | | | +|NanoMethViz |? | | | | +|NanoStringDiff |? | | | | +|nanotatoR |? | | | | +|NanoTube |? | | | | +|NBAMSeq |? | | | | +|ncdfFlow |? | | | | +|ncGTW |? | | | | +|ndexr |? | | | | +|Nebulosa |? | | | | +|NestLink |? | | | | +|NetActivity |? | | | | +|netDx |? | | | | +|nethet |? | | | | +|netOmics |? | | | | +|netSmooth |? | | | | +|netZooR |? | | | | +|NewWave |? | | | | +|ngsReports |? | | | | +|nipalsMCIA |? | | | | +|nnSVG |? | | | | +|NoRCE |? | | | | +|NormalyzerDE |? | | | | +|normr |? | | | | +|NPARC |? | | | | +|nucleoSim |? | | | | +|nucleR |? | | | | +|nuCpos |? | | | | +|nullranges |? | | | | +|NxtIRFdata |? | | | | +|ObMiTi |? | | | | +|OGRE |? | | | | +|omada |? | | | | +|OmaDB |? | | | | +|omicsPrint |? | | | | +|Omixer |? | | | | +|OmnipathR |? | | | | +|ompBAM |? | | | | +|oncomix |? | | | | +|oncoscanR |? | | | | +|OncoScore |? | | | | +|OncoSimulR |? | | | | +|onlineFDR |? | | | | +|ontoProc |? | | | | +|ontoProcData |? | | | | +|openCyto |? | | | | +|openPrimeR |? | | | | +|OPWeight |? | | | | +|ORFik |? | | | | +|Organism.dplyr |? | | | | +|orthogene |? | | | | +|orthos |? | | | | +|orthosData |? | | | | +|Oscope |? | | | | +|OUTRIDER |? | | | | +|OutSplice |? | | | | +|OVESEG |? | | | | +|packFinder |? | | | | +|padma |? | | | | +|PAIRADISE |? | | | | +|pairedGSEA |? | | | | +|PanomiR |? | | | | +|PanViz |? | | | | +|pareg |? | | | | +|parody |? | | | | +|partCNV |? | | | | +|PasillaTranscriptExpr |? | | | | +|PathoStat |? | | | | +|pathwayPCA |? | | | | +|paxtoolsr |? | | | | +|pcaExplorer |? | | | | +|PCAtools |? | | | | +|PCHiCdata |? | | | | +|PDATK |? | | | | +|peakPantheR |? | | | | +|pengls |? | | | | +|periodicDNA |? | | | | +|pgca |? | | | | +|phantasus |? | | | | +|phantasusLite |? | | | | +|PharmacoGx |? | | | | +|phenomis |? | | | | +|phenopath |? | | | | +|philr |? | | | | +|PhIPData |? | | | | +|phosphonormalizer |? | | | | +|PhosR |? | | | | +|PhyloProfile |? | | | | +|phyloseq |? | | | | +|pipeFrame |? | | | | +|planet |? | | | | +|planttfhunter |? | | | | +|plasmut |? | | | | +|plotgardener |? | | | | +|plotGrouper |? | | | | +|plyinteractions |? | | | | +|plyranges |? | | | | +|pmp |? | | | | +|PoDCall |? | | | | +|pogos |? | | | | +|POMA |? | | | | +|POWSC |? | | | | +|ppcseq |? | | | | +|pqsfinder |? | | | | +|pram |? | | | | +|preciseTAD |? | | | | +|proActiv |? | | | | +|proDA |? | | | | +|profileplyr |? | | | | +|progeny |? | | | | +|projectR |? | | | | +|pRoloc |? | | | | +|pRolocdata |? | | | | +|pRolocGUI |? | | | | +|Prostar |? | | | | +|proteinProfiles |? | | | | +|ProteoDisco |? | | | | +|ProtGenerics |? | | | | +|psichomics |? | | | | +|PSMatch |? | | | | +|psygenet2r |? | | | | +|ptairData |? | | | | +|ptairMS |? | | | | +|PureCN |? | | | | +|PWMEnrich |? | | | | +|qckitfastq |? | | | | +|QFeatures |? | | | | +|qmtools |? | | | | +|qPLEXanalyzer |? | | | | +|qsea |? | | | | +|qsmooth |? | | | | +|qsvaR |? | | | | +|QTLExperiment |? | | | | +|Qtlizer |? | | | | +|quantiseqr |? | | | | +|QuasR |? | | | | +|raer |? | | | | +|raerdata |? | | | | +|RaggedExperiment |? | | | | +|RAIDS |? | | | | +|RandomWalkRestartMH |? | | | | +|randRotation |? | | | | +|RAREsim |? | | | | +|rawrr |? | | | | +|RBioFormats |? | | | | +|Rbowtie |? | | | | +|Rbowtie2 |? | | | | +|Rbwa |? | | | | +|RCAS |? | | | | +|rcellminer |? | | | | +|rcellminerData |? | | | | +|RCM |? | | | | +|Rcollectl |? | | | | +|Rcpi |? | | | | +|Rcwl |? | | | | +|RcwlPipelines |? | | | | +|RCX |? | | | | +|rDGIdb |? | | | | +|ReactomeContentService4R |? | | | | +|ReactomeGraph4R |? | | | | +|ReactomeGSA |? | | | | +|ReactomePA |? | | | | +|rebook |? | | | | +|receptLoss |? | | | | +|reconsi |? | | | | +|recount |? | | | | +|recount3 |? | | | | +|recountmethylation |? | | | | +|RedisParam |? | | | | +|regionalpcs |? | | | | +|RegionalST |? | | | | +|regioneR |? | | | | +|regioneReloaded |? | | | | +|regsplice |? | | | | +|regutools |? | | | | +|RepViz |? | | | | +|ResidualMatrix |? | | | | +|RESOLVE |? | | | | +|restfulSE |? | | | | +|retrofit |? | | | | +|rexposome |? | | | | +|Rfastp |? | | | | +|rGenomeTracks |? | | | | +|RgnTX |? | | | | +|rgoslin |? | | | | +|rGREAT |? | | | | +|rhdf5 |? | | | | +|rhdf5client |? | | | | +|Rhisat2 |? | | | | +|RiboCrypt |? | | | | +|RiboProfiling |? | | | | +|ribor |? | | | | +|ribosomeProfilingQC |? | | | | +|RIVER |? | | | | +|RLSeq |? | | | | +|rmelting |? | | | | +|Rmmquant |? | | | | +|rmspc |? | | | | +|RNAAgeCalc |? | | | | +|rnaEditr |? | | | | +|RNAmodR |? | | | | +|RNAmodR.AlkAnilineSeq |? | | | | +|RNAmodR.Data |? | | | | +|RNAmodR.ML |? | | | | +|RNAmodR.RiboMethSeq |? | | | | +|RNAseqCovarImpute |? | | | | +|RnaSeqSampleSize |? | | | | +|roar |? | | | | +|RolDE |? | | | | +|rols |? | | | | +|ropls |? | | | | +|ROSeq |? | | | | +|ROTS |? | | | | +|rprimer |? | | | | +|rpx |? | | | | +|Rqc |? | | | | +|rrvgo |? | | | | +|rScudo |? | | | | +|rsemmed |? | | | | +|RSeqAn |? | | | | +|rstanarm |2.26.1 |1 | | | +|RTCGA |? | | | | +|Rtpca |? | | | | +|runibic |? | | | | +|RVS |? | | | | +|rWikiPathways |? | | | | +|S4Arrays |? | | | | +|sangeranalyseR |? | | | | +|SARC |? | | | | +|satuRn |? | | | | +|SBGNview |? | | | | +|ScaledMatrix |? | | | | +|scanMiR |? | | | | +|scanMiRApp |? | | | | +|scAnnotatR |? | | | | +|scATAC.Explorer |? | | | | +|scater |? | | | | +|scatterHatch |? | | | | +|scBFA |? | | | | +|scBubbletree |? | | | | +|scCB2 |? | | | | +|sccomp |? | | | | +|scDblFinder |? | | | | +|scDDboost |? | | | | +|scDesign3 |? | | | | +|scFeatureFilter |? | | | | +|scGPS |? | | | | +|schex |? | | | | +|scider |? | | | | +|scifer |? | | | | +|scMerge |? | | | | +|scMET |? | | | | +|scMultiome |? | | | | +|scone |? | | | | +|Sconify |? | | | | +|SCOPE |? | | | | +|scoreInvHap |? | | | | +|scp |? | | | | +|scPCA |? | | | | +|scpdata |? | | | | +|scPipe |? | | | | +|scran |? | | | | +|scReClassify |? | | | | +|scRecover |? | | | | +|screenCounter |? | | | | +|ScreenR |? | | | | +|scRNAseq |? | | | | +|scRNAseqApp |? | | | | +|scruff |? | | | | +|scry |? | | | | +|scShapes |? | | | | +|scTensor |? | | | | +|scTGIF |? | | | | +|scTreeViz |? | | | | +|scuttle |? | | | | +|scviR |? | | | | +|SDAMS |? | | | | +|segmenter |? | | | | +|selectKSigs |? | | | | +|semisup |? | | | | +|seq.hotSPOT |? | | | | +|seqArchR |? | | | | +|seqCAT |? | | | | +|SeqGate |? | | | | +|seqLogo |? | | | | +|seqpac |? | | | | +|seqsetvis |? | | | | +|SeqSQC |? | | | | +|sesame |? | | | | +|sesameData |? | | | | +|sevenbridges |? | | | | +|sevenC |? | | | | +|SFEData |? | | | | +|SharedObject |? | | | | +|shinyepico |? | | | | +|shinyMethyl |? | | | | +|SIAMCAT |? | | | | +|sights |? | | | | +|signatureSearch |? | | | | +|signifinder |? | | | | +|SimBu |? | | | | +|SIMLR |? | | | | +|simona |? | | | | +|simpleSeg |? | | | | +|simplifyEnrichment |? | | | | +|SingleCellExperiment |? | | | | +|singleCellTK |? | | | | +|SingleMoleculeFootprinting |? | | | | +|SingleR |? | | | | +|singscore |? | | | | +|sitePath |? | | | | +|slalom |? | | | | +|slingshot |? | | | | +|SMAD |? | | | | +|smokingMouse |? | | | | +|snapcount |? | | | | +|snifter |? | | | | +|SNPediaR |? | | | | +|soGGi |? | | | | +|SomaScan.db |? | | | | +|SomaticCancerAlterations |? | | | | +|SomaticSignatures |? | | | | +|SOMNiBUS |? | | | | +|Spaniel |? | | | | +|sparrow |? | | | | +|SparseArray |? | | | | +|sparseMatrixStats |? | | | | +|sparsenetgls |? | | | | +|SparseSignatures |? | | | | +|spaSim |? | | | | +|SpatialCPie |? | | | | +|spatialDE |? | | | | +|SpatialDecon |? | | | | +|SpatialExperiment |? | | | | +|SpatialFeatureExperiment |? | | | | +|spatialLIBD |? | | | | +|SpatialOmicsOverlay |? | | | | +|spatzie |? | | | | +|speckle |? | | | | +|Spectra |? | | | | +|SpectralTAD |? | | | | +|SPIAT |? | | | | +|SpidermiR |? | | | | +|spiky |? | | | | +|splatter |? | | | | +|SpliceWiz |? | | | | +|SplicingFactory |? | | | | +|SpotClean |? | | | | +|SPOTlight |? | | | | +|SPsimSeq |? | | | | +|SQLDataFrame |? | | | | +|srnadiff |? | | | | +|sSNAPPY |? | | | | +|ssPATHS |? | | | | +|ssrch |? | | | | +|stageR |? | | | | +|standR |? | | | | +|StarBioTrek |? | | | | +|Statial |? | | | | +|statTarget |? | | | | +|STdeconvolve |? | | | | +|stJoincount |? | | | | +|strandCheckR |? | | | | +|struct |? | | | | +|Structstrings |? | | | | +|structToolbox |? | | | | +|StructuralVariantAnnotation |? | | | | +|subSeq |? | | | | +|SummarizedBenchmark |? | | | | +|SummarizedExperiment |? | | | | +|supersigs |? | | | | +|surfaltr |? | | | | +|sva |? | | | | +|svaNUMT |? | | | | +|svaRetro |? | | | | +|SVMDO |? | | | | +|SWATH2stats |? | | | | +|swfdr |? | | | | +|switchde |? | | | | +|synapsis |? | | | | +|synapter |? | | | | +|synaptome.db |? | | | | +|synlet |? | | | | +|SynMut |? | | | | +|syntenet |? | | | | +|systemPipeR |? | | | | +|systemPipeShiny |? | | | | +|systemPipeTools |? | | | | +|TabulaMurisData |? | | | | +|TabulaMurisSenisData |? | | | | +|tadar |? | | | | +|TADCompare |? | | | | +|TAPseq |? | | | | +|target |? | | | | +|TargetDecoy |? | | | | +|tartare |? | | | | +|TBSignatureProfiler |? | | | | +|TCGAbiolinks |? | | | | +|TCGAutils |? | | | | +|TCGAWorkflowData |? | | | | +|TCseq |? | | | | +|TDbasedUFE |? | | | | +|TDbasedUFEadv |? | | | | +|TEKRABber |? | | | | +|tenXplore |? | | | | +|ternarynet |? | | | | +|terraTCGAdata |? | | | | +|TFBSTools |? | | | | +|TFutils |? | | | | +|tidybulk |? | | | | +|tidySingleCellExperiment |? | | | | +|tidySummarizedExperiment |? | | | | +|TileDBArray |? | | | | +|timecoursedata |? | | | | +|timeOmics |? | | | | +|TimiRGeN |? | | | | +|TissueEnrich |? | | | | +|tissueTreg |? | | | | +|TMixClust |? | | | | +|TnT |? | | | | +|tomoda |? | | | | +|tomoseqr |? | | | | +|topconfects |? | | | | +|topdownr |? | | | | +|ToxicoGx |? | | | | +|TPP |? | | | | +|TPP2D |? | | | | +|tradeSeq |? | | | | +|TrajectoryUtils |? | | | | +|transcriptR |? | | | | +|transformGamPoi |? | | | | +|transite |? | | | | +|transomics2cytoscape |? | | | | +|traviz |? | | | | +|treeio |? | | | | +|treekoR |? | | | | +|TreeSummarizedExperiment |? | | | | +|TREG |? | | | | +|tricycle |? | | | | +|TriDimRegression |1.0.2 |1 | | | +|tripr |? | | | | +|triptych |0.1.2 |1 | | | +|tRNA |? | | | | +|tRNAdbImport |? | | | | +|tRNAscanImport |? | | | | +|TRONCO |? | | | | +|TSAR |? | | | | +|TSCAN |? | | | | +|ttgsea |? | | | | +|TVTB |? | | | | +|twoddpcr |? | | | | +|txcutr |? | | | | +|tximeta |? | | | | +|tximport |? | | | | +|UMI4Cats |? | | | | +|uncoverappLib |? | | | | +|UniProtKeywords |? | | | | +|Uniquorn |? | | | | +|universalmotif |? | | | | +|updateObject |? | | | | +|uSORT |? | | | | +|VAExprs |? | | | | +|VarCon |? | | | | +|VariantExperiment |? | | | | +|VCFArray |? | | | | +|VDJdive |? | | | | +|velociraptor |? | | | | +|veloviz |? | | | | +|VennDetail |? | | | | +|VERSO |? | | | | +|vidger |? | | | | +|vissE |? | | | | +|Voyager |? | | | | +|VplotR |? | | | | +|vsclust |? | | | | +|vsn |? | | | | +|waddR |? | | | | +|weitrix |? | | | | +|wiggleplotr |? | | | | +|wpm |? | | | | +|wppi |? | | | | +|xcms |? | | | | +|xcore |? | | | | +|XNAString |? | | | | +|yamss |? | | | | +|YAPSA |? | | | | +|yarn |? | | | | +|zellkonverter |? | | | | +|zinbwave |? | | | | +|ZygosityPredictor |? | | | | + ## New problems (1) -|package |version |error |warning |note | -|:--------|:-------|:------|:-------|:----| -|[APCalign](problems.md#apcalign)|0.1.3 |__+1__ | |1 | +|package |version |error |warning |note | +|:-------|:-------|:------|:-------|:----| +|[miWQS](problems.md#miwqs)|0.4.4 |__+1__ |-1 | | diff --git a/revdep/cran.md b/revdep/cran.md index e96943212..c96c9471e 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,15 +1,28 @@ ## revdepcheck results -We checked 10 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 9101 reverse dependencies (7910 from CRAN + 1191 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 1 new problems - * We failed to check 0 packages + * We failed to check 11 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* APCalign - checking tests ... ERROR +* miWQS + checking re-building of vignette outputs ... ERROR +### Failed to check + +* bayesdfa (NA) +* Boom (NA) +* ctsem (NA) +* fdaPDE (NA) +* gllvm (NA) +* glmmrOptim (NA) +* loon.shiny (NA) +* loon.tourr (NA) +* rstanarm (NA) +* TriDimRegression (NA) +* triptych (NA) diff --git a/revdep/problems.md b/revdep/problems.md index c2bf65032..b195c8ce3 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,48 +1,68 @@ -# APCalign +# miWQS
-* Version: 0.1.3 -* GitHub: https://github.com/traitecoevo/APCalign -* Source code: https://github.com/cran/APCalign -* Date/Publication: 2023-11-16 22:43:53 UTC -* Number of recursive dependencies: 97 +* Version: 0.4.4 +* GitHub: https://github.com/phargarten2/miWQS +* Source code: https://github.com/cran/miWQS +* Date/Publication: 2021-04-02 21:50:02 UTC +* Number of recursive dependencies: 152 -Run `revdepcheck::cloud_details(, "APCalign")` for more info +Run `revdepcheck::cloud_details(, "miWQS")` for more info
## Newly broken -* checking tests ... ERROR +* checking re-building of vignette outputs ... ERROR ``` - Running ‘testthat.R’ - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > # This file is part of the standard setup for testthat. - > # It is recommended that you do not modify it. - > # - > # Where should you do additional test configuration? - > # Learn more about the roles of various files in: - > # * https://r-pkgs.org/tests.html - > # * https://testthat.r-lib.org/reference/test_package.html#special-files + Error(s) in re-building vignettes: + --- re-building ‘README.Rmd’ using rmarkdown + tlmgr: package repository https://ctan.mirrors.hoobly.com/systems/texlive/tlnet (verified) + [1/1, ??:??/??:??] install: grffile [4k] + running mktexlsr ... + done running mktexlsr. + tlmgr: package log updated: /opt/TinyTeX/texmf-var/web2c/tlmgr.log + tlmgr: command log updated: /opt/TinyTeX/texmf-var/web2c/tlmgr-commands.log + tlmgr: package repository https://mirror.mwt.me/ctan/systems/texlive/tlnet (verified) + [1/2, ??:??/??:??] install: biblatex [249k] ... - 6. │ └─dplyr:::check_nth_default(default, x = x) - 7. │ └─vctrs::vec_init(x) - 8. └─vctrs:::stop_scalar_type(``(NULL), "x", ``(vec_init())) - 9. └─vctrs:::stop_vctrs(...) - 10. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call) - - [ FAIL 1 | WARN 0 | SKIP 0 | PASS 85 ] - Error: Test failures - In addition: There were 18 warnings (use warnings() to see them) - Execution halted + Warning: (biblatex) and rerun LaTeX afterwards. + Error: processing vignette 'README.Rmd' failed with diagnostics: + Failed to build the bibliography via biber + --- failed re-building ‘README.Rmd’ + + SUMMARY: processing the following file failed: + ‘README.Rmd’ + + Error: Vignette re-building failed. + Execution halted ``` -## In both +## Newly fixed -* checking data for non-ASCII characters ... NOTE +* checking re-building of vignette outputs ... WARNING ``` - Note: found 4 marked UTF-8 strings + Error(s) in re-building vignettes: + ... + --- re-building ‘README.Rmd’ using rmarkdown + + tlmgr: Remote database (rev 68993) seems to be older than local (rev 68995 of texlive-scripts); please use different mirror or wait a day or so. + Warning in system2("tlmgr", args, ...) : + running command ''tlmgr' search --file --global '/grffile.sty'' had status 1 + ! LaTeX Error: File `grffile.sty' not found. + + ! Emergency stop. + ... + + Error: processing vignette 'README.Rmd' failed with diagnostics: + LaTeX failed to compile /tmp/workdir/miWQS/old/miWQS.Rcheck/vign_test/miWQS/vignettes/README.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See README.log for more info. + --- failed re-building ‘README.Rmd’ + + SUMMARY: processing the following file failed: + ‘README.Rmd’ + + Error: Vignette re-building failed. + Execution halted ```