From c8bbc0df6910d722ca047b7d82f1ecc90f91c444 Mon Sep 17 00:00:00 2001 From: hadley Date: Fri, 29 Dec 2017 07:35:34 -0600 Subject: [PATCH] Re-run again to check pr change --- revdep/README.md | 1242 ++++++++++++++++++++++---------------------- revdep/problems.md | 715 ++++++++++++++----------- 2 files changed, 1037 insertions(+), 920 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 13ffbd24..be97378d 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -9,646 +9,656 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-12-20 | +|date |2017-12-29 | # Dependencies -|package |old |new |Δ | -|:--------|:-----|:-----|:--| -|stringr |1.2.0 |1.3.0 |* | -|glue |NA |1.2.0 |* | -|magrittr |1.5 |1.5 | | -|stringi |1.1.6 |1.1.6 | | +|package |old |new |Δ | +|:--------|:-----|:----------|:--| +|stringr |1.2.0 |1.2.0.9000 |* | +|glue |NA |1.2.0 |* | +|magrittr |1.5 |1.5 | | +|stringi |1.1.6 |1.1.6 | | # Revdeps -## Couldn't check (18) +## Couldn't check (23) |package |version |error |warning |note | |:------------------------------------------|:-------|:---------|:-------|:----| +|aqp |? | | | | |[ATACseqQC](problems.md#atacseqqc) |1.0.5 |1 | |1 | |[BiGGR](problems.md#biggr) |1.12.0 |1 | |1 | -|[DeepBlueR](problems.md#deepbluer) |1.2.10 |2 | | | +|[DeepBlueR](problems.md#deepbluer) |1.2.10 |2 |1 | | |[dynamichazard](problems.md#dynamichazard) |0.5.1 |1 | | | |[EasyMARK](problems.md#easymark) |1.0 |1 | | | |[erccdashboard](problems.md#erccdashboard) |1.10.0 |1 | | | |[fastLink](problems.md#fastlink) |0.2.0 |1 | | | |[FRESA.CAD](problems.md#fresacad) |2.2.1 |1 | | | |[HydeNet](problems.md#hydenet) |0.10.6 |-2 __+1__ |-1 | | -|[ideal](problems.md#ideal) |1.0.0 |1 | |2 | -|[imager](problems.md#imager) |0.40.2 |1 | |1 | +|[IATscores](problems.md#iatscores) |0.1-2 |__+1__ | |-1 | +|imager |? | | | | +|ISOweek |? | | | | |[monocle](problems.md#monocle) |2.4.0 |__+1__ |-1 |-1 | |[morse](problems.md#morse) |2.2.0 |1 | | | -|[mvGST](problems.md#mvgst) |1.10.0 |1 | |1 | +|nucim |? | | | | +|PhysActBedRest |? | | | | +|[psygenet2r](problems.md#psygenet2r) |1.9.1 |1 | |3 | |[redcapAPI](problems.md#redcapapi) |1.3 |1 | | | +|rmonad |? | | | | |[rsunlight](problems.md#rsunlight) |0.4.2 |__+1__ | |1 | +|simr |? | | | | |[TPP](problems.md#tpp) |3.4.3 |1 | |3 | -|IATscores |? | | | | -## Broken (4) +## Broken (5) -|package |version |error |warning |note | -|:----------------------------------------|:-------|:------|:-------|:------| -|[BioInstaller](problems.md#bioinstaller) |0.3.1 |__+1__ | | | -|[FedData](problems.md#feddata) |2.5.0 |__+1__ | | | -|[knitr](problems.md#knitr) |1.17 | | |__+1__ | -|[xpose](problems.md#xpose) |0.4.0 |__+1__ | |1 | +|package |version |error |warning |note | +|:----------------------------------------|:-------|:-----------|:-------|:--------| +|[alpine](problems.md#alpine) |1.2.0 |__+1__ | | | +|[BioInstaller](problems.md#bioinstaller) |0.3.1 |__+1__ | | | +|[GetITRData](problems.md#getitrdata) |0.6 | |__+1__ | | +|[knitr](problems.md#knitr) |1.18 | | |__+1__ | +|[TCGAbiolinks](problems.md#tcgabiolinks) |2.5.9 |1 -1 __+1__ |__+1__ |2 __+1__ | -## All (593) +## All (597) -|package |version |error |warning |note | -|:----------------------------------------------------------------|:---------|:---------|:-------|:------| -|abcrf |1.7 | | | | -|[abjutils](problems.md#abjutils) |0.0.1 |1 | |1 | -|acs |2.1.2 | | | | -|aemo |0.2.0 | | | | -|[afex](problems.md#afex) |0.18-0 | | |1 | -|[AFM](problems.md#afm) |1.2.2 | |1 | | -|[aire.zmvm](problems.md#airezmvm) |0.5.0 | | |1 | -|ALA4R |1.5.6 | | | | -|[algstat](problems.md#algstat) |0.0.2 | | |1 | -|[alphavantager](problems.md#alphavantager) |0.1.0 | | |1 | -|alpine |1.2.0 | | | | -|[AmostraBrasil](problems.md#amostrabrasil) |1.2 | | |1 | -|[AnDE](problems.md#ande) |1.0 | | |2 | -|antaresRead |2.0.2 | | | | -|apa |0.2.0 | | | | -|ApacheLogProcessor |0.2.2 | | | | -|APSIM |0.9.2 | | | | -|aqp |1.15 | | | | -|arsenal |0.6.1 | | | | -|[asciiSetupReader](problems.md#asciisetupreader) |1.2 | | |1 | -|aslib |0.1 | | | | -|assignPOP |1.1.3 | | | | -|[ATACseqQC](problems.md#atacseqqc) |1.0.5 |1 | |1 | -|atlantistools |0.4.3 | | | | -|auk |0.1.0 | | | | -|[badgecreatr](problems.md#badgecreatr) |0.1.0 | | |1 | -|[banocc](problems.md#banocc) |1.0.0 | | |1 | -|[banR](problems.md#banr) |0.2.0 | | |1 | -|[banxicoR](problems.md#banxicor) |0.9.0 | | |1 | -|[basecallQC](problems.md#basecallqc) |1.0.1 | |1 | | -|BatchGetSymbols |1.2 | | | | -|BayesFactor |0.9.12-2 | | | | -|[bea.R](problems.md#bear) |1.0.4 | | |1 | -|[beepr](problems.md#beepr) |1.2 | | |1 | -|[betalink](problems.md#betalink) |2.2.1 | | |1 | -|BETS |0.3.3 | | | | -|bib2df |1.0.0 | | | | -|bibliometrix |1.8 | | | | -|bibtex |0.4.2 | | | | -|[BiGGR](problems.md#biggr) |1.12.0 |1 | |1 | -|[bioCancer](problems.md#biocancer) |1.4.0 | |2 |2 | -|[BiocWorkflowTools](problems.md#biocworkflowtools) |1.2.0 |1 | |1 | -|biogeo |1.0 | | | | -|[BioInstaller](problems.md#bioinstaller) |0.3.1 |__+1__ | | | -|[biomartr](problems.md#biomartr) |0.5.2 |2 |1 | | -|[blastula](problems.md#blastula) |0.1 | | |1 | -|[blkbox](problems.md#blkbox) |1.0 | | |2 | -|blogdown |0.4 | | | | -|blscrapeR |3.1.1 | | | | -|bold |0.5.0 | | | | -|[boostr](problems.md#boostr) |1.0.0 | | |2 | -|boxr |0.3.4 | | | | -|BradleyTerryScalable |0.1.0 | | | | -|[branchpointer](problems.md#branchpointer) |1.0.0 |1 |2 | | -|[breathtestcore](problems.md#breathtestcore) |0.4.0 | | |1 | -|breathteststan |0.4.0 | | | | -|[bridgesampling](problems.md#bridgesampling) |0.4-0 | |1 | | -|broom |0.4.3 | | | | -|brr |1.0.0 | | | | -|[bsplus](problems.md#bsplus) |0.1.0 | | |1 | -|[BTLLasso](problems.md#btllasso) |0.1-7 | | |1 | -|[Causata](problems.md#causata) |4.2-0 | |1 |2 | -|[cellscape](problems.md#cellscape) |1.0.0 | |2 |3 | -|censusr |0.0.3 | | | | -|[chipenrich](problems.md#chipenrich) |2.0.1 | |1 | | -|choroplethr |3.6.1 | | | | -|[CIAAWconsensus](problems.md#ciaawconsensus) |1.2 | | |1 | -|[CINdex](problems.md#cindex) |1.4.0 | | |2 | -|civis |1.1.1 | | | | -|ck37r |1.0.0 | | | | -|ClimClass |2.1.0 | | | | -|CLME |2.0-8 | | | | -|CoFRA |0.1002 | | | | -|CollapsABEL |0.10.11 | | | | -|colormap |0.1.4 | | | | -|commentr |1.0.4 | | | | -|[compcodeR](problems.md#compcoder) |1.12.0 | | |3 | -|[configr](problems.md#configr) |0.3.1.1 | | |1 | -|[congressbr](problems.md#congressbr) |0.1.1 | | |1 | -|[consensusSeekeR](problems.md#consensusseeker) |1.4.0 | |1 | | -|[CRANsearcher](problems.md#cransearcher) |1.0.0 | | |1 | -|[crossmeta](problems.md#crossmeta) |1.2.0 | |1 |3 | -|crtests |0.2.1 | | | | -|cruts |0.3 | | | | -|[ctsGE](problems.md#ctsge) |1.2.0 | |1 | | -|[cummeRbund](problems.md#cummerbund) |2.18.0 |1 |1 |6 | -|[customProDB](problems.md#customprodb) |1.16.0 |1 | |4 | -|cymruservices |0.2.0 | | | | -|cytominer |0.1.0 | | | | -|[d3Tree](problems.md#d3tree) |0.2.0 | | |1 | -|[dartR](problems.md#dartr) |1.0 | |1 |1 | -|[data.tree](problems.md#datatree) |0.7.3 |1 |1 | | -|[datacheck](problems.md#datacheck) |1.2.2 | | |2 | -|datadogr |0.1.1 | | | | -|dataone |2.1.0 | | | | -|dataPreparation |0.3.4 | | | | -|[datasus](problems.md#datasus) |0.4.0 | | |1 | -|[DeepBlueR](problems.md#deepbluer) |1.2.10 |2 | | | -|[DeLorean](problems.md#delorean) |1.2.5 | |2 | | -|descriptr |0.3.0 | | | | -|detector |0.1.0 | | | | -|[DEXSeq](problems.md#dexseq) |1.22.0 | | |1 | -|DiagrammeR |0.9.2 | | | | -|diceR |0.3.1 | | | | -|difconet |1.0-4 | | | | -|distcomp |1.0-1 | | | | -|dMod |0.4 | | | | -|docopt |0.4.5 | | | | -|docxtools |0.1.1 | | | | -|[dotwhisker](problems.md#dotwhisker) |0.3.0 | | |1 | -|dplR |1.6.6 | | | | -|[dplyrAssist](problems.md#dplyrassist) |0.1.0 | | |1 | -|drake |4.4.0 | | | | -|[driftR](problems.md#driftr) |1.0.0 | | |1 | -|drLumi |0.1.2 | | | | -|[dtree](problems.md#dtree) |0.2.3 | |1 | | -|[dynamichazard](problems.md#dynamichazard) |0.5.1 |1 | | | -|[EasyMARK](problems.md#easymark) |1.0 |1 | | | -|[eclust](problems.md#eclust) |0.1.0 | | |1 | -|edeaR |0.7.2 | | | | -|eemR |0.1.5 | | | | -|[eeptools](problems.md#eeptools) |1.1.0 | |1 | | -|[eiCompare](problems.md#eicompare) |2.1 | |1 | | -|[elementR](problems.md#elementr) |1.3.3 |1 | | | -|emuR |0.2.3 | | | | -|enaR |3.0.0 | | | | -|[ENCODExplorer](problems.md#encodexplorer) |2.2.1 | | |3 | -|envDocument |2.4.0 | | | | -|[epitable](problems.md#epitable) |0.1.2 | | |1 | -|[eqs2lavaan](problems.md#eqs2lavaan) |3.0 | | |1 | -|[erccdashboard](problems.md#erccdashboard) |1.10.0 |1 | | | -|ess |0.0.1 | | | | -|etl |0.3.7 | | | | -|eurostat |3.1.5 | | | | -|evaluate |0.10.1 | | | | -|[EventPointer](problems.md#eventpointer) |1.0.0 | |1 |2 | -|[EventStudy](problems.md#eventstudy) |0.34 | | |2 | -|Evomorph |0.9 | | | | -|exampletestr |1.1.1 | | | | -|[exsic](problems.md#exsic) |1.1.1 | | |1 | -|eyelinker |0.1 | | | | -|ez |4.4-0 | | | | -|[fastLink](problems.md#fastlink) |0.2.0 |1 | | | -|fbar |0.3.4 | | | | -|[fbRanks](problems.md#fbranks) |2.0 | | |2 | -|[FedData](problems.md#feddata) |2.5.0 |__+1__ | | | -|fergm |0.2.1 | | | | -|[FFTrees](problems.md#fftrees) |1.3.5 | | |1 | -|Fgmutils |0.9.4 | | | | -|filesstrings |2.0.1 | | | | -|[fitbitScraper](problems.md#fitbitscraper) |0.1.8 | |1 | | -|[fivethirtyeight](problems.md#fivethirtyeight) |0.3.0 | | |3 | -|[flextable](problems.md#flextable) |0.4.0 | | |1 | -|[flowWorkspace](problems.md#flowworkspace) |3.24.4 | |1 |7 | -|[fontMPlus](problems.md#fontmplus) |0.1.1 | |1 |1 | -|[fragilityindex](problems.md#fragilityindex) |0.1.0 | | |1 | -|frequencyConnectedness |0.1.6 | | | | -|[FRESA.CAD](problems.md#fresacad) |2.2.1 |1 | | | -|fungible |1.5 | | | | -|futureheatwaves |1.0.3 | | | | -|fuzzyjoin |0.1.3 | | | | -|[GADMTools](problems.md#gadmtools) |2.1-1 | |1 |1 | -|[gaiah](problems.md#gaiah) |0.0.2 | | |1 | -|[games](problems.md#games) |1.1.2 | | |1 | -|[gastempt](problems.md#gastempt) |0.4.01 | | |1 | -|GCalignR |1.0.0 | | | | -|[genderizeR](problems.md#genderizer) |2.0.0 | | |1 | -|genemodel |1.1.0 | | | | -|geniusr |1.0.0 | | | | -|[GenomicInteractions](problems.md#genomicinteractions) |1.10.0 | | |1 | -|[GenomicTools](problems.md#genomictools) |0.2.6 | |1 | | -|geoparser |0.1.1 | | | | -|geotopbricks |1.4 | | | | -|GERGM |0.11.2 | | | | -|GetDFPData |0.5 | | | | -|GetHFData |1.5 | | | | -|GetITRData |0.6 | | | | -|GetLattesData |0.9 | | | | -|GetTDData |1.3 | | | | -|gfcanalysis |1.4 | | | | -|[ggenealogy](problems.md#ggenealogy) |0.3.0 | | |2 | -|[ggformula](problems.md#ggformula) |0.6 | |1 |1 | -|[ggmap](problems.md#ggmap) |2.6.1 | | |1 | -|[ggplotAssist](problems.md#ggplotassist) |0.1.3 | | |1 | -|ggplotgui |1.0.0 | | | | -|[ggraptR](problems.md#ggraptr) |1.0 | | |1 | -|gitlabr |0.9 | | | | -|glue |1.2.0 | | | | -|[GOexpress](problems.md#goexpress) |1.10.0 | | |3 | -|[gogamer](problems.md#gogamer) |0.4.3 |1 | | | -|googlesheets |0.2.2 | | | | -|gphmm |0.99.0 | | | | -|[Greg](problems.md#greg) |1.2 | |1 |2 | -|gsheet |0.4.2 | | | | -|GSIF |0.5-4 | | | | -|[GUIgems](problems.md#guigems) |0.1 | |1 |1 | -|[gutenbergr](problems.md#gutenbergr) |0.1.3 | | |1 | -|[hddtools](problems.md#hddtools) |0.7 |1 |1 | | -|heemod |0.9.2 | | | | -|[highcharter](problems.md#highcharter) |0.5.0 | | |1 | -|[HistogramTools](problems.md#histogramtools) |0.3.2 | | |2 | -|hoardeR |0.9.2 | | | | -|[htmlTable](problems.md#htmltable) |1.11.0 | | |1 | -|[HTSSIP](problems.md#htssip) |1.3.0 |1 |1 |2 | -|HURDAT |0.1.0 | | | | -|[hurricaneexposure](problems.md#hurricaneexposure) |0.0.1 | | |1 | -|hybridModels |0.2.15 | | | | -|[HydeNet](problems.md#hydenet) |0.10.6 |-2 __+1__ |-1 | | -|hypercube |0.1.0 | | | | -|[icd](problems.md#icd) |2.3.1 | | |2 | -|IDCard |0.3.0 | | | | -|[ideal](problems.md#ideal) |1.0.0 |1 | |2 | -|ijtiff |0.2.0 | | | | -|[imager](problems.md#imager) |0.40.2 |1 | |1 | -|inferr |0.2.0 | | | | -|io |0.2.4 | | | | -|[IONiseR](problems.md#ioniser) |2.0.0 | |1 |2 | -|ipumsr |0.1.1 | | | | -|IRISMustangMetrics |2.0.8 | | | | -|IRISSeismic |1.4.6 | | | | -|[ISOweek](problems.md#isoweek) |0.6-2 | | |1 | -|[jpmesh](problems.md#jpmesh) |1.0.1 | | |3 | -|[JunctionSeq](problems.md#junctionseq) |1.6.0 | | |3 | -|[kableExtra](problems.md#kableextra) |0.6.1 | |1 | | -|kehra |0.1 | | | | -|keyringr |0.4.0 | | | | -|kgschart |1.3.5 | | | | -|[knitr](problems.md#knitr) |1.17 | | |__+1__ | -|kntnr |0.4.1 | | | | -|[kokudosuuchi](problems.md#kokudosuuchi) |0.4.1 | | |2 | -|[KoNLP](problems.md#konlp) |0.80.1 | | |1 | -|LAGOSNE |1.1.0 | | | | -|latex2exp |0.4.0 | | | | -|[leaflet.esri](problems.md#leafletesri) |0.2 | | |1 | -|[leaflet.extras](problems.md#leafletextras) |0.2 | | |1 | -|lemon |0.3.1 | | | | -|lero.lero |0.1 | | | | -|lettercase |0.13.1 | | | | -|[lidR](problems.md#lidr) |1.3.1 | | |1 | -|lifelogr |0.1.0 | | | | -|liftr |0.8 | | | | -|LindenmayeR |0.1.13 | | | | -|linear.tools |1.3.0 | | | | -|lmem.gwaser |0.1.0 | | | | -|lmem.qtler |0.1.1 | | | | -|lmomPi |0.5.0 | | | | -|[LowMACA](problems.md#lowmaca) |1.8.0 |1 |1 |2 | -|[lubridate](problems.md#lubridate) |1.7.1 |1 | |1 | -|m2r |1.0.0 | | | | -|madrat |1.22.1 | | | | -|[Maeswrap](problems.md#maeswrap) |1.7 | |1 | | -|mailR |0.4.1 | | | | -|managelocalrepo |0.1.5 | | | | -|[mapscape](problems.md#mapscape) |1.0.0 | |1 |1 | -|[MARSS](problems.md#marss) |3.9 | | |2 | -|[MAST](problems.md#mast) |1.2.1 | |1 |1 | -|matlabr |1.4.3 | | | | -|mau |0.1.0 | | | | -|MazamaSpatialUtils |0.5.2 | | | | -|MazamaWebUtils |0.1.5 | | | | -|mem |2.11 | | | | -|[memapp](problems.md#memapp) |2.6 | | |1 | -|metacoder |0.1.3 | | | | -|[metagear](problems.md#metagear) |0.4 |1 | | | -|[metagenomeFeatures](problems.md#metagenomefeatures) |1.8.1 | | |2 | -|[MetaIntegrator](problems.md#metaintegrator) |1.0.3 | |1 | | -|[MetamapsDB](problems.md#metamapsdb) |0.0.2 | | |1 | -|[MethTargetedNGS](problems.md#methtargetedngs) |1.8.0 | | |1 | -|mglR |0.1.0 | | | | -|mgm |1.2-2 | | | | -|micromapST |1.1.1 | | | | -|[miRLAB](problems.md#mirlab) |1.6.0 | | |1 | -|[miRNAtap](problems.md#mirnatap) |1.10.0 |2 | |4 | -|miscset |1.1.0 | | | | -|[missMethyl](problems.md#missmethyl) |1.10.0 | |1 |2 | -|[mlbgameday](problems.md#mlbgameday) |0.0.1 | | |1 | -|[mmnet](problems.md#mmnet) |1.13.0 |1 | | | -|[modeval](problems.md#modeval) |0.1.3 | |1 | | -|[MODIStsp](problems.md#modistsp) |1.3.3.1 |1 | | | -|modules |0.6.0 | | | | -|[monocle](problems.md#monocle) |2.4.0 |__+1__ |-1 |-1 | -|[morse](problems.md#morse) |2.2.0 |1 | | | -|[motifbreakR](problems.md#motifbreakr) |1.6.0 | | |2 | -|mpoly |1.0.5 | | | | -|[mrMLM](problems.md#mrmlm) |2.1 |1 | | | -|MSbox |1.0 | | | | -|[msPurity](problems.md#mspurity) |1.2.0 | |2 |3 | -|mtconnectR |1.1.0 | | | | -|[mtk](problems.md#mtk) |1.0 | |1 |3 | -|[mudata2](problems.md#mudata2) |1.0.0 | | |1 | -|muir |0.1.0 | | | | -|muRL |0.1-11 | | | | -|[mvGST](problems.md#mvgst) |1.10.0 |1 | |1 | -|nandb |0.2.1 | | | | -|narray |0.3.2 | | | | -|[nauf](problems.md#nauf) |1.1.0 | |1 | | -|net.security |0.3.0 | | | | -|netgen |1.3 | | | | -|networkreporting |0.1.1 | | | | -|neuroim |0.0.6 | | | | -|[NFP](problems.md#nfp) |0.99.2 | | |2 | -|ngstk |0.1.1.1 | | | | -|nhanesA |0.6.4.3.3 | | | | -|[Nippon](problems.md#nippon) |0.6.5 | | |2 | -|[NMF](problems.md#nmf) |0.20.6 | |2 |2 | -|nmfgpu4R |0.2.5.2 | | | | -|[NNS](problems.md#nns) |0.3.8.1 | |1 | | -|NNTbiomarker |0.29.11 | | | | -|[noaastormevents](problems.md#noaastormevents) |0.1.0 | | |2 | -|nparACT |0.8 | | | | -|nscprepr |0.1.1 | | | | -|nucim |1.0.0 | | | | -|nyctaxi |0.0.1 | | | | -|oai |0.2.2 | | | | -|olsrr |0.4.0 | | | | -|OpenRepGrid |0.1.10 | | | | -|optim.functions |0.1 | | | | -|optiRum |0.37.3 | | | | -|optiSel |2.0 | | | | -|optiSolve |0.1 | | | | -|optparse |1.4.4 | | | | -|orgR |0.9.0 | | | | -|osmose |0.1.0 | | | | -|outreg |0.2.2 | | | | -|[P2C2M](problems.md#p2c2m) |0.7.6 | | |3 | -|packagedocs |0.4.0 | | | | -|pafdR |1.0 | | | | -|[parsemsf](problems.md#parsemsf) |0.1.1 | | |1 | -|[patchSynctex](problems.md#patchsynctex) |0.1-4 | | |1 | -|[PATHChange](problems.md#pathchange) |1.0 | | |1 | -|[PepPrep](problems.md#pepprep) |1.1.0 | | |1 | -|PersomicsArray |1.0 | | | | -|[PGA](problems.md#pga) |1.6.0 |1 -1 |1 |3 | -|phenomap |1.0.1 | | | | -|phenopix |2.3.1 | | | | -|phrasemachine |1.1.2 | | | | -|phybreak |0.2.0 | | | | -|PhysActBedRest |1.0 | | | | -|pipefittr |0.1.2 | | | | -|pixiedust |0.8.1 | | | | -|pkgcopier |0.0.1 | | | | -|[pkgmaker](problems.md#pkgmaker) |0.22 | |1 |2 | -|[PKPDmisc](problems.md#pkpdmisc) |2.1.1 | | |1 | -|Plasmidprofiler |0.1.6 | | | | -|plotKML |0.5-8 | | | | -|plotROC |2.2.0 | | | | -|pMineR |0.31 | | | | -|pmml |1.5.3 | | | | -|[pointblank](problems.md#pointblank) |0.1 | | |1 | -|politeness |0.1.2 | | | | -|pollstR |2.0.0 | | | | -|[polywog](problems.md#polywog) |0.4-0 | | |2 | -|postGIStools |0.2.1 | | | | -|powerbydesign |1.0.3 | | | | -|pre |0.4 | | | | -|predatory |1.2 | | | | -|[primerTree](problems.md#primertree) |1.0.3 | | |1 | -|[prisonbrief](problems.md#prisonbrief) |0.1.0 | | |1 | -|Prize |1.6.0 | | | | -|processmapR |0.2.1 | | | | -|[profr](problems.md#profr) |0.3.1 | | |2 | -|profvis |0.3.4 | | | | -|ProjectTemplate |0.8 | | | | -|promote |1.0.0 | | | | -|proPubBills |0.1 | | | | -|[proustr](problems.md#proustr) |0.2.1 | | |1 | -|prozor |0.2.3 | | | | -|pryr |0.1.3 | | | | -|psichomics |1.2.1 | | | | -|[psygenet2r](problems.md#psygenet2r) |1.9.1 | |1 |3 | -|[ptstem](problems.md#ptstem) |0.0.3 | | |1 | -|PubMedWordcloud |0.3.5 | | | | -|[pubprint](problems.md#pubprint) |0.2.1 | | |2 | -|[PWFSLSmoke](problems.md#pwfslsmoke) |0.99.33 | |1 | | -|[pxR](problems.md#pxr) |0.42.2 | |1 | | -|pxweb |0.6.3 | | | | -|QCAtools |0.2.3 | | | | -|qrcode |0.1.1 | | | | -|qualtRics |2.2 | | | | -|[quantoptr](problems.md#quantoptr) |0.1.2 | | |1 | -|[QuaternaryProd](problems.md#quaternaryprod) |1.4.0 | |1 |1 | -|[quipu](problems.md#quipu) |1.9.0 | | |1 | -|R2ucare |1.0.0 | | | | -|[radiant.model](problems.md#radiantmodel) |0.8.0 | | |1 | -|ragtop |0.5 | | | | -|randomcoloR |1.1.0 | | | | -|rapport |1.0 | | | | -|ratios |1.1.0 | | | | -|[rattle](problems.md#rattle) |5.1.0 |1 | | | -|[rAvis](problems.md#ravis) |0.1.4 | | |1 | -|[rcellminer](problems.md#rcellminer) |1.8.0 |2 |1 |3 | -|[rClinicalCodes](problems.md#rclinicalcodes) |1.0.1 | | |2 | -|rcrossref |0.8.0 | | | | -|[rcv](problems.md#rcv) |0.2.1 | | |1 | -|RDML |0.9-9 | | | | -|readJDX |0.2.3 | | | | -|[recoder](problems.md#recoder) |0.1 | | |1 | -|[redcapAPI](problems.md#redcapapi) |1.3 |1 | | | -|RefManageR |0.14.20 | | | | -|[reportRx](problems.md#reportrx) |1.0 | | |1 | -|reshape2 |1.4.3 | | | | -|RevEcoR |0.99.3 | | | | -|revengc |1.0.0 | | | | -|rex |1.1.2 | | | | -|rfordummies |0.1.3 | | | | -|RGENERATEPREC |1.2 | | | | -|rgeopat2 |0.1.4 | | | | -|Rilostat |0.2 | | | | -|RJafroc |0.1.1 | | | | -|RLogicalOps |0.1 | | | | -|[rmarkdown](problems.md#rmarkdown) |1.8 | | |1 | -|rmonad |0.4.0 | | | | -|[RndTexExams](problems.md#rndtexexams) |1.4 | |1 | | -|[RNeXML](problems.md#rnexml) |2.0.8 | | |1 | -|[rngtools](problems.md#rngtools) |1.2.4 | |1 |2 | -|Rnightlights |0.1.4 | | | | -|[Rnits](problems.md#rnits) |1.10.0 | | |2 | -|rNOMADS |2.3.8 | | | | -|rnrfa |1.3.0 | | | | -|robotstxt |0.5.2 | | | | -|[rodham](problems.md#rodham) |0.1.1 | | |2 | -|rollply |0.5.0 | | | | -|ropercenter |0.1.0 | | | | -|roxygen2 |6.0.1 | | | | -|rpcdsearch |1.0 | | | | -|rpdo |0.2.2 | | | | -|Rpolyhedra |0.1.0 | | | | -|rPraat |1.0.8 | | | | -|[rprime](problems.md#rprime) |0.1.0 | | |1 | -|rpubchem |1.5.10 | | | | -|[RQGIS](problems.md#rqgis) |1.0.2 | |1 | | -|RSDA |2.0.2 | | | | -|RSentiment |2.2.1 | | | | -|[rsgcc](problems.md#rsgcc) |1.0.6 |1 | | | -|RSiteCatalyst |1.4.13 | | | | -|rslp |0.1.0 | | | | -|RSMET |1.2.9 | | | | -|rsnps |0.2.0 | | | | -|rSQM |1.2.42 | | | | -|[rsunlight](problems.md#rsunlight) |0.4.2 |__+1__ | |1 | -|rsurfer |0.2 | | | | -|rtide |0.0.4 | | | | -|[rtimicropem](problems.md#rtimicropem) |1.3 | | |1 | -|rUnemploymentData |1.1.0 | | | | -|rusda |1.0.8 | | | | -|ryouready |0.4 | | | | -|[sasMap](problems.md#sasmap) |1.0.0 | | |1 | -|satscanMapper |1.0.0 | | | | -|sbtools |1.1.6 | | | | -|scholar |0.1.4 | | | | -|[SciencesPo](problems.md#sciencespo) |1.4.1 | |1 |1 | -|scientoText |0.1 | | | | -|[sdcTable](problems.md#sdctable) |0.22.8 |1 | | | -|searchConsoleR |0.2.1 | | | | -|secr |3.1.3 | | | | -|SeerMapper |1.2.0 | | | | -|selectr |0.3-1 | | | | -|[SeqVarTools](problems.md#seqvartools) |1.14.0 | | |1 | -|[Seurat](problems.md#seurat) |2.1.0 | |1 | | -|sevenbridges |1.6.4 | | |-1 | -|[ShinyItemAnalysis](problems.md#shinyitemanalysis) |1.2.3 | | |1 | -|ShinyTester |0.1.0 | | | | -|[SICtools](problems.md#sictools) |1.6.0 | |1 |3 | -|[sidrar](problems.md#sidrar) |0.2.4 | | |1 | -|sim1000G |1.33 | | | | -|simcausal |0.5.4 | | | | -|simPH |1.3.10 | | | | -|[simPop](problems.md#simpop) |1.0.0 | |1 |1 | -|simr |1.0.3 | | | | -|[sincell](problems.md#sincell) |1.8.0 | |1 |2 | -|sjmisc |2.6.3 | | | | -|smpic |0.1.0 | | | | -|snakecase |0.5.1 | | | | -|SnakeCharmR |1.0.7 | | | | -|snpReady |0.9.4 | | | | -|SocialMediaLab |0.23.2 | | | | -|[SomaticCancerAlterations](problems.md#somaticcanceralterations) |1.12.0 | | |2 | -|[sophisthse](problems.md#sophisthse) |0.7.0 | | |1 | -|[SoundexBR](problems.md#soundexbr) |1.2 | | |1 | -|spAddins |0.2.0 | | | | -|[spant](problems.md#spant) |0.6.0 | |1 |1 | -|spatsurv |1.1 | | | | -|spellcheckr |0.1.2 | | | | -|sperrorest |2.1.1 | | | | -|[spind](problems.md#spind) |2.1.1 | | |1 | -|sqliter |0.1.0 | | | | -|[sqlutils](problems.md#sqlutils) |1.2 | | |4 | -|[ssh.utils](problems.md#sshutils) |1.0 | | |2 | -|SSRA |0.1-0 | | | | -|[Stack](problems.md#stack) |2.0-1 | | |1 | -|[stacomiR](problems.md#stacomir) |0.5.3 |1 | | | -|standardize |0.2.1 | | | | -|[starmie](problems.md#starmie) |0.1.2 | | |2 | -|statar |0.6.5 | | | | -|[stationaRy](problems.md#stationary) |0.4.1 | | |1 | -|[statquotes](problems.md#statquotes) |0.2.2 | | |1 | -|[statsDK](problems.md#statsdk) |0.1.1 | | |1 | -|stm |1.3.0 | | | | -|stormwindmodel |0.1.0 | | | | -|[stplanr](problems.md#stplanr) |0.2.2 | | |1 | -|stremr |0.4 | | | | -|stringformattr |0.1.2 | | | | -|striprtf |0.5.1 | | | | -|subspace |1.0.4 | | | | -|surveybootstrap |0.0.1 | | | | -|surveydata |0.2.0 | | | | -|survtmle |1.0.0 | | | | -|[sweep](problems.md#sweep) |0.2.0 | | |1 | -|sweidnumbr |1.4.1 | | | | -|swirl |2.4.3 | | | | -|[swirlify](problems.md#swirlify) |0.5.1 |1 | | | -|[syuzhet](problems.md#syuzhet) |1.0.4 | | |1 | -|tangram |0.3.2 | | | | -|[taRifx](problems.md#tarifx) |1.0.6 | | |3 | -|[taxa](problems.md#taxa) |0.2.0 | | |1 | -|taxize |0.9.0 | | | | -|[TBFmultinomial](problems.md#tbfmultinomial) |0.1.1 | |1 | | -|[TCGAbiolinks](problems.md#tcgabiolinks) |2.5.9 |2 |1 |3 | -|[TCGAbiolinksGUI](problems.md#tcgabiolinksgui) |1.2.1 | |1 |3 | -|TcGSA |0.10.5 | | | | -|templates |0.2.0 | | | | -|TexExamRandomizer |1.2.2 | | | | -|[text2vec](problems.md#text2vec) |0.5.0 | | |3 | -|textmineR |2.0.6 | | | | -|[textreuse](problems.md#textreuse) |0.1.4 | | |1 | -|tibbletime |0.0.2 | | | | -|tidycensus |0.3.1 | | | | -|[tidyquant](problems.md#tidyquant) |0.5.3 |1 |2 |1 | -|tidytext |0.1.5 | | | | -|[tidyverse](problems.md#tidyverse) |1.2.1 | | |1 | -|tigris |0.5.3 | | | | -|[tikzDevice](problems.md#tikzdevice) |0.10-1 | |1 | | -|timelineR |0.1.0 | | | | -|[timescape](problems.md#timescape) |1.0.0 | |1 |3 | -|[timetk](problems.md#timetk) |0.1.0 | | |1 | -|[TIN](problems.md#tin) |1.8.0 | | |1 | -|TLBC |1.0 | | | | -|tmlenet |0.1.0 | | | | -|[tmuxr](problems.md#tmuxr) |0.1.0 |1 | | | -|touch |0.1-3 | | | | -|[TPP](problems.md#tpp) |3.4.3 |1 | |3 | -|[tracktables](problems.md#tracktables) |1.10.0 | |1 |1 | -|[translateSPSS2R](problems.md#translatespss2r) |1.0.0 | | |1 | -|treeman |1.1.1 | | | | -|tropr |0.1.2 | | | | -|tspmeta |1.2 | | | | -|TSTr |1.2 | | | | -|[tumblR](problems.md#tumblr) |1.1 | | |1 | -|uavRmp |0.5.1 | | | | -|[ucbthesis](problems.md#ucbthesis) |1.0 | | |1 | -|ukds |0.1.0 | | | | -|Uniquorn |1.4.2 | | | | -|unpivotr |0.3.0 | | | | -|uptasticsearch |0.1.0 | | | | -|urlshorteneR |0.9.2 | | | | -|[usmap](problems.md#usmap) |0.2.1 | | |3 | -|utilsIPEA |0.0.5 | | | | -|vagalumeR |0.1.1 | | | | -|[valaddin](problems.md#valaddin) |0.1.2 | | |1 | -|validaRA |0.1.1 | | | | -|valr |0.3.1 | | | | -|[vardpoor](problems.md#vardpoor) |0.9.11 |1 | | | -|[VarfromPDB](problems.md#varfrompdb) |2.2.7 | |1 | | -|vcfR |1.6.0 | | | | -|VDAP |2.0.0 | | | | -|vembedr |0.1.3 | | | | -|vennplot |1.0 | | | | -|[vetools](problems.md#vetools) |1.3-28 | | |1 | -|vfcp |1.4.0 | | | | -|ViSiElse |1.2.0 | | | | -|vkR |0.1 | | | | -|vortexR |1.1.4 | | | | -|vows |0.5 | | | | -|[vqtl](problems.md#vqtl) |1.2.0 | | |1 | -|[wavClusteR](problems.md#wavcluster) |2.10.0 | |1 |3 | -|webchem |0.3.0 | | | | -|webTRISr |0.1.0 | | | | -|[wikilake](problems.md#wikilake) |0.3 | | |1 | -|wikipediatrend |1.1.14 | | | | -|WikiSocio |0.7.0 | | | | -|[wingui](problems.md#wingui) |0.2 | |1 | | -|[wordbankr](problems.md#wordbankr) |0.2.0 | |1 |1 | -|[wsrf](problems.md#wsrf) |1.7.17 | |1 | | -|[wux](problems.md#wux) |2.2-1 | |1 | | -|x.ent |1.1.7 | | | | -|x12 |1.9.0 | | | | -|[x12GUI](problems.md#x12gui) |0.13.0 |1 | | | -|xesreadR |0.2.2 | | | | -|Xplortext |1.1.0 | | | | -|[xpose](problems.md#xpose) |0.4.0 |__+1__ | |1 | -|yhatr |0.15.1 | | | | -|[ztype](problems.md#ztype) |0.1.0 | | |1 | -|IATscores |? | | | | +|package |version |error |warning |note | +|:----------------------------------------------------------------|:---------|:-----------|:-------|:--------| +|abcrf |1.7 | | | | +|[abjutils](problems.md#abjutils) |0.0.1 |1 | |1 | +|acs |2.1.2 | | | | +|aemo |0.2.0 | | | | +|[afex](problems.md#afex) |0.18-0 | |1 |1 | +|[AFM](problems.md#afm) |1.2.2 | |1 | | +|[aire.zmvm](problems.md#airezmvm) |0.5.0 | | |1 | +|ALA4R |1.5.6 | | | | +|[algstat](problems.md#algstat) |0.0.2 | | |1 | +|[alphavantager](problems.md#alphavantager) |0.1.0 | | |1 | +|[alpine](problems.md#alpine) |1.2.0 |__+1__ | | | +|[AmostraBrasil](problems.md#amostrabrasil) |1.2 | | |1 | +|[AnDE](problems.md#ande) |1.0 | | |2 | +|antaresRead |2.0.2 | | | | +|apa |0.2.0 | | | | +|ApacheLogProcessor |0.2.2 | | | | +|APSIM |0.9.2 | | | | +|aqp |? | | | | +|arsenal |0.6.1 | | | | +|[asciiSetupReader](problems.md#asciisetupreader) |1.2 | | |1 | +|aslib |0.1 | | | | +|assignPOP |1.1.3 | | | | +|[ATACseqQC](problems.md#atacseqqc) |1.0.5 |1 | |1 | +|atlantistools |0.4.3 | | | | +|auk |0.1.0 | | | | +|[badgecreatr](problems.md#badgecreatr) |0.1.0 | | |1 | +|[banocc](problems.md#banocc) |1.0.0 | |1 |1 | +|[banR](problems.md#banr) |0.2.0 | | |1 | +|[banxicoR](problems.md#banxicor) |0.9.0 | | |1 | +|[basecallQC](problems.md#basecallqc) |1.0.1 | |1 | | +|BatchGetSymbols |1.2 | | | | +|BayesFactor |0.9.12-2 | | | | +|[bea.R](problems.md#bear) |1.0.4 | | |1 | +|[beepr](problems.md#beepr) |1.2 | | |1 | +|[betalink](problems.md#betalink) |2.2.1 | | |1 | +|BETS |0.3.3 | | | | +|bib2df |1.0.0 | | | | +|bibliometrix |1.8 | | | | +|bibtex |0.4.2 | | | | +|[BiGGR](problems.md#biggr) |1.12.0 |1 | |1 | +|[bioCancer](problems.md#biocancer) |1.4.0 | |2 |2 | +|[BiocWorkflowTools](problems.md#biocworkflowtools) |1.2.0 |1 | |1 | +|biogeo |1.0 | | | | +|[BioInstaller](problems.md#bioinstaller) |0.3.1 |__+1__ | | | +|[biomartr](problems.md#biomartr) |0.5.2 |-1 |1 | | +|[blastula](problems.md#blastula) |0.1 | | |1 | +|[blkbox](problems.md#blkbox) |1.0 | | |2 | +|blogdown |0.4 | | | | +|blscrapeR |3.1.1 | | | | +|bold |0.5.0 | | | | +|[boostr](problems.md#boostr) |1.0.0 | | |2 | +|boxr |0.3.4 | | | | +|BradleyTerryScalable |0.1.0 | | | | +|[branchpointer](problems.md#branchpointer) |1.0.0 | |1 | | +|[breathtestcore](problems.md#breathtestcore) |0.4.0 | | |1 | +|breathteststan |0.4.0 | | | | +|[bridgesampling](problems.md#bridgesampling) |0.4-0 | |1 | | +|broom |0.4.3 | | | | +|brr |1.0.0 | | | | +|[bsplus](problems.md#bsplus) |0.1.0 | | |1 | +|[BTLLasso](problems.md#btllasso) |0.1-7 | | |1 | +|[Causata](problems.md#causata) |4.2-0 | |1 |2 | +|[cellscape](problems.md#cellscape) |1.0.0 | |2 |3 | +|censusr |0.0.3 | | | | +|[chipenrich](problems.md#chipenrich) |2.0.1 | |1 | | +|choroplethr |3.6.1 | | | | +|[CIAAWconsensus](problems.md#ciaawconsensus) |1.2 | | |1 | +|[CINdex](problems.md#cindex) |1.4.0 | | |2 | +|civis |1.1.1 | | | | +|ck37r |1.0.0 | | | | +|ClimClass |2.1.0 | | | | +|[CLME](problems.md#clme) |2.0-8 | |1 | | +|CoFRA |0.1002 | | | | +|CollapsABEL |0.10.11 | | | | +|colormap |0.1.4 | | | | +|commentr |1.0.4 | | | | +|[compcodeR](problems.md#compcoder) |1.12.0 | | |3 | +|[configr](problems.md#configr) |0.3.2 | | |1 | +|[congressbr](problems.md#congressbr) |0.1.1 | | |1 | +|[consensusSeekeR](problems.md#consensusseeker) |1.4.0 | |1 | | +|[CRANsearcher](problems.md#cransearcher) |1.0.0 | | |1 | +|[crossmeta](problems.md#crossmeta) |1.2.0 | |1 |3 | +|crtests |0.2.1 | | | | +|cruts |0.3 | | | | +|[ctsGE](problems.md#ctsge) |1.2.0 | |1 | | +|[cummeRbund](problems.md#cummerbund) |2.18.0 |1 |1 |6 | +|[customProDB](problems.md#customprodb) |1.16.0 |1 | |4 | +|cymruservices |0.2.0 | | | | +|cytominer |0.1.0 | | | | +|[d3Tree](problems.md#d3tree) |0.2.0 | | |1 | +|[dartR](problems.md#dartr) |1.0 | |1 |1 | +|[data.tree](problems.md#datatree) |0.7.3 |1 |1 | | +|[datacheck](problems.md#datacheck) |1.2.2 | | |2 | +|datadogr |0.1.1 | | | | +|dataone |2.1.0 | | | | +|dataPreparation |0.3.4 | | | | +|[datasus](problems.md#datasus) |0.4.0 | | |1 | +|[DeepBlueR](problems.md#deepbluer) |1.2.10 |2 |1 | | +|[DeLorean](problems.md#delorean) |1.2.5 | |2 | | +|descriptr |0.3.0 | | | | +|detector |0.1.0 | | | | +|[DEXSeq](problems.md#dexseq) |1.22.0 | | |1 | +|DiagrammeR |0.9.2 | | | | +|diceR |0.3.1 | | | | +|difconet |1.0-4 | | | | +|distcomp |1.0-1 | | | | +|dMod |0.4 | | | | +|docopt |0.4.5 | | | | +|docxtools |0.1.1 | | | | +|[dotwhisker](problems.md#dotwhisker) |0.3.0 | | |1 | +|dplR |1.6.6 | | | | +|[dplyrAssist](problems.md#dplyrassist) |0.1.0 | | |1 | +|drake |4.4.0 | | | | +|[driftR](problems.md#driftr) |1.0.0 | | |1 | +|drLumi |0.1.2 | | | | +|[dtree](problems.md#dtree) |0.2.3 | |1 | | +|[dynamichazard](problems.md#dynamichazard) |0.5.1 |1 | | | +|[EasyMARK](problems.md#easymark) |1.0 |1 | | | +|[eclust](problems.md#eclust) |0.1.0 | | |1 | +|edeaR |0.7.2 | | | | +|eemR |0.1.5 | | | | +|[eeptools](problems.md#eeptools) |1.1.0 | |1 | | +|[eiCompare](problems.md#eicompare) |2.1 | |1 | | +|[elementR](problems.md#elementr) |1.3.3 |1 | | | +|emuR |0.2.3 | | | | +|enaR |3.0.0 | | | | +|[ENCODExplorer](problems.md#encodexplorer) |2.2.1 | | |3 | +|envDocument |2.4.0 | | | | +|[epitable](problems.md#epitable) |0.1.2 | | |1 | +|[eqs2lavaan](problems.md#eqs2lavaan) |3.0 | | |1 | +|[erccdashboard](problems.md#erccdashboard) |1.10.0 |1 | | | +|ess |0.0.1 | | | | +|etl |0.3.7 | | | | +|eurostat |3.1.5 | | | | +|evaluate |0.10.1 | | | | +|[EventPointer](problems.md#eventpointer) |1.0.0 | |1 |2 | +|[EventStudy](problems.md#eventstudy) |0.34 | | |2 | +|Evomorph |0.9 | | | | +|exampletestr |1.1.1 | | | | +|[exsic](problems.md#exsic) |1.1.1 | | |1 | +|eyelinker |0.1 | | | | +|ez |4.4-0 | | | | +|[fastLink](problems.md#fastlink) |0.2.0 |1 | | | +|fbar |0.3.4 | | | | +|[fbRanks](problems.md#fbranks) |2.0 | | |2 | +|FedData |2.5.0 |-1 | | | +|[fergm](problems.md#fergm) |0.2.1 | |1 | | +|[FFTrees](problems.md#fftrees) |1.3.5 | | |1 | +|Fgmutils |0.9.4 | | | | +|filesstrings |2.0.1 | | | | +|[fitbitScraper](problems.md#fitbitscraper) |0.1.8 | |1 | | +|[fivethirtyeight](problems.md#fivethirtyeight) |0.3.0 | | |2 | +|[flextable](problems.md#flextable) |0.4.0 | | |1 | +|[flowWorkspace](problems.md#flowworkspace) |3.24.4 | |1 |7 | +|[fontMPlus](problems.md#fontmplus) |0.1.1 | |1 |1 | +|[fragilityindex](problems.md#fragilityindex) |0.1.0 | | |1 | +|[frequencyConnectedness](problems.md#frequencyconnectedness) |0.1.6 | |1 | | +|[FRESA.CAD](problems.md#fresacad) |2.2.1 |1 | | | +|fungible |1.5 | | | | +|futureheatwaves |1.0.3 | | | | +|fuzzyjoin |0.1.3 | | | | +|[GADMTools](problems.md#gadmtools) |2.1-1 | |1 |1 | +|[gaiah](problems.md#gaiah) |0.0.2 | | |1 | +|[games](problems.md#games) |1.1.2 | |1 |1 | +|[gastempt](problems.md#gastempt) |0.4.01 | | |1 | +|GCalignR |1.0.0 | | | | +|[genderizeR](problems.md#genderizer) |2.0.0 | | |1 | +|genemodel |1.1.0 | | | | +|geniusr |1.0.0 | | | | +|[GenomicInteractions](problems.md#genomicinteractions) |1.10.0 | | |1 | +|[GenomicTools](problems.md#genomictools) |0.2.6 | |1 | | +|geoparser |0.1.1 | | | | +|geotopbricks |1.4 | | | | +|GERGM |0.11.2 | | | | +|GetDFPData |0.5 | | | | +|GetHFData |1.5 | | | | +|[GetITRData](problems.md#getitrdata) |0.6 | |__+1__ | | +|GetLattesData |0.9 | | | | +|GetTDData |1.3 | | | | +|gfcanalysis |1.4 | | | | +|[ggenealogy](problems.md#ggenealogy) |0.3.0 | | |2 | +|[ggformula](problems.md#ggformula) |0.6 | |1 |1 | +|[ggmap](problems.md#ggmap) |2.6.1 | | |1 | +|[ggplotAssist](problems.md#ggplotassist) |0.1.3 | | |1 | +|ggplotgui |1.0.0 | | | | +|[ggraptR](problems.md#ggraptr) |1.0 | | |1 | +|gitlabr |0.9 | | | | +|glue |1.2.0 | | | | +|[GOexpress](problems.md#goexpress) |1.10.0 | | |2 -1 | +|[gogamer](problems.md#gogamer) |0.4.3 |1 | | | +|googlesheets |0.2.2 | | | | +|gphmm |0.99.0 | | | | +|[Greg](problems.md#greg) |1.2 | |1 |2 | +|gsheet |0.4.2 | | | | +|GSIF |0.5-4 | | | | +|[GUIgems](problems.md#guigems) |0.1 | |1 |1 | +|[gutenbergr](problems.md#gutenbergr) |0.1.3 | | |1 | +|[hddtools](problems.md#hddtools) |0.7 |1 |1 | | +|heemod |0.9.2 | | | | +|[highcharter](problems.md#highcharter) |0.5.0 | | |1 | +|[HistogramTools](problems.md#histogramtools) |0.3.2 | | |2 | +|hoardeR |0.9.2 | | | | +|[htmlTable](problems.md#htmltable) |1.11.1 | | |1 | +|[HTSSIP](problems.md#htssip) |1.3.0 |1 |1 |2 | +|HURDAT |0.1.0 | | | | +|[hurricaneexposure](problems.md#hurricaneexposure) |0.0.1 | | |1 | +|hybridModels |0.2.15 | | | | +|[HydeNet](problems.md#hydenet) |0.10.6 |-2 __+1__ |-1 | | +|[hydroscoper](problems.md#hydroscoper) |0.1.0 | | |1 | +|hypercube |0.1.0 | | | | +|[IATscores](problems.md#iatscores) |0.1-2 |__+1__ | |-1 | +|[icd](problems.md#icd) |2.3.1 | | |2 | +|IDCard |0.3.0 | | | | +|[ideal](problems.md#ideal) |1.0.0 | | |2 | +|ijtiff |0.2.0 | | | | +|imager |? | | | | +|inferr |0.2.0 | | | | +|io |0.2.4 | | | | +|[IONiseR](problems.md#ioniser) |2.0.0 | |1 |2 | +|ipumsr |0.1.1 | | | | +|IRISMustangMetrics |2.0.8 | | | | +|IRISSeismic |1.4.6 | | | | +|ISOweek |? | | | | +|[jpmesh](problems.md#jpmesh) |1.0.1 | | |2 | +|[JunctionSeq](problems.md#junctionseq) |1.6.0 | | |3 | +|[kableExtra](problems.md#kableextra) |0.6.1 | |1 | | +|kehra |0.1 | | | | +|keyringr |0.4.0 | | | | +|kgschart |1.3.5 | | | | +|[knitr](problems.md#knitr) |1.18 | | |__+1__ | +|kntnr |0.4.1 | | | | +|[kokudosuuchi](problems.md#kokudosuuchi) |0.4.1 | | |2 | +|[KoNLP](problems.md#konlp) |0.80.1 | | |1 | +|LAGOSNE |1.1.0 | | | | +|latex2exp |0.4.0 | | | | +|[leaflet.esri](problems.md#leafletesri) |0.2 | | |1 | +|[leaflet.extras](problems.md#leafletextras) |0.2 | | |1 | +|lemon |0.3.1 | | | | +|lero.lero |0.1 | | | | +|lettercase |0.13.1 | | | | +|[lidR](problems.md#lidr) |1.3.1 | | |1 | +|lifelogr |0.1.0 | | | | +|liftr |0.8 | | | | +|LindenmayeR |0.1.13 | | | | +|linear.tools |1.3.0 | | | | +|lmem.gwaser |0.1.0 | | | | +|lmem.qtler |0.1.1 | | | | +|lmomPi |0.5.0 | | | | +|[LowMACA](problems.md#lowmaca) |1.8.0 |1 |1 |2 | +|[lubridate](problems.md#lubridate) |1.7.1 |1 | |1 | +|m2r |1.0.0 | | | | +|madrat |1.22.1 | | | | +|[Maeswrap](problems.md#maeswrap) |1.7 | |1 | | +|mailR |0.4.1 | | | | +|managelocalrepo |0.1.5 | | | | +|[mapscape](problems.md#mapscape) |1.0.0 | |1 |1 | +|[MARSS](problems.md#marss) |3.9 | | |2 | +|[MAST](problems.md#mast) |1.2.1 | |1 |1 | +|matlabr |1.4.3 | | | | +|mau |0.1.0 | | | | +|MazamaSpatialUtils |0.5.2 | | | | +|MazamaWebUtils |0.1.5 | | | | +|mem |2.11 | | | | +|[memapp](problems.md#memapp) |2.6 | | |1 | +|metacoder |0.1.3 | | | | +|[metagear](problems.md#metagear) |0.4 |1 | | | +|[metagenomeFeatures](problems.md#metagenomefeatures) |1.8.1 | | |2 | +|[MetaIntegrator](problems.md#metaintegrator) |1.0.3 | |1 | | +|[MetamapsDB](problems.md#metamapsdb) |0.0.2 | | |1 | +|[MethTargetedNGS](problems.md#methtargetedngs) |1.8.0 | | |1 | +|mglR |0.1.0 | | | | +|mgm |1.2-2 | | | | +|micromapST |1.1.1 | | | | +|[miRLAB](problems.md#mirlab) |1.6.0 | | |1 | +|[miRNAtap](problems.md#mirnatap) |1.10.0 |2 | |4 | +|miscset |1.1.0 | | | | +|[missMethyl](problems.md#missmethyl) |1.10.0 | |1 |2 | +|[mlbgameday](problems.md#mlbgameday) |0.0.1 | | |1 | +|[mmnet](problems.md#mmnet) |1.13.0 |1 | | | +|[modeval](problems.md#modeval) |0.1.3 | |1 | | +|[MODIStsp](problems.md#modistsp) |1.3.3.1 |1 | | | +|modules |0.6.0 | | | | +|[monocle](problems.md#monocle) |2.4.0 |__+1__ |-1 |-1 | +|[morse](problems.md#morse) |2.2.0 |1 | | | +|[motifbreakR](problems.md#motifbreakr) |1.6.0 | | |2 | +|mpoly |1.0.5 | | | | +|[mrMLM](problems.md#mrmlm) |2.1 |1 | | | +|MSbox |1.0 | | | | +|[msPurity](problems.md#mspurity) |1.2.0 | |2 |3 | +|mtconnectR |1.1.0 | | | | +|[mtk](problems.md#mtk) |1.0 | |1 |3 | +|[mudata2](problems.md#mudata2) |1.0.0 | | |1 | +|muir |0.1.0 | | | | +|muRL |0.1-11 | | | | +|[mvGST](problems.md#mvgst) |1.10.0 | | |1 | +|nandb |0.2.1 | | | | +|narray |0.3.2 | | | | +|[nauf](problems.md#nauf) |1.1.0 | |1 | | +|net.security |0.3.0 | | | | +|netgen |1.3 | | | | +|networkreporting |0.1.1 | | | | +|neuroim |0.0.6 | | | | +|[NFP](problems.md#nfp) |0.99.2 | | |2 | +|ngstk |0.1.1.1 | | | | +|nhanesA |0.6.4.3.3 | | | | +|[Nippon](problems.md#nippon) |0.6.5 | | |2 | +|[NMF](problems.md#nmf) |0.20.6 | |2 |2 | +|nmfgpu4R |0.2.5.2 | | | | +|[NNS](problems.md#nns) |0.3.8.1 | |1 | | +|NNTbiomarker |0.29.11 | | | | +|[noaastormevents](problems.md#noaastormevents) |0.1.0 | | |2 | +|nparACT |0.8 | | | | +|nscprepr |0.1.1 | | | | +|nucim |? | | | | +|nyctaxi |0.0.1 | | | | +|oai |0.2.2 | | | | +|olsrr |0.4.0 | | | | +|OpenRepGrid |0.1.10 | | | | +|optim.functions |0.1 | | | | +|optiRum |0.37.3 | | | | +|optiSel |2.0 | | | | +|optiSolve |0.1 | | | | +|optparse |1.4.4 | | | | +|orgR |0.9.0 | | | | +|osmose |0.1.0 | | | | +|outreg |0.2.2 | | | | +|[P2C2M](problems.md#p2c2m) |0.7.6 | | |3 | +|packagedocs |0.4.0 | | | | +|pafdR |1.0 | | | | +|[parsemsf](problems.md#parsemsf) |0.1.1 | | |1 | +|[patchSynctex](problems.md#patchsynctex) |0.1-4 | | |1 | +|[PATHChange](problems.md#pathchange) |1.0 | | |1 | +|[PepPrep](problems.md#pepprep) |1.1.0 | | |1 | +|PersomicsArray |1.0 | | | | +|[PGA](problems.md#pga) |1.6.0 |1 |1 |3 | +|phenomap |1.0.1 | | | | +|phenopix |2.3.1 | | | | +|phrasemachine |1.1.2 | | | | +|phybreak |0.2.0 | | | | +|PhysActBedRest |? | | | | +|pipefittr |0.1.2 | | | | +|pixiedust |0.8.1 | | | | +|pkgcopier |0.0.1 | | | | +|[pkgmaker](problems.md#pkgmaker) |0.22 | |1 |2 | +|[PKPDmisc](problems.md#pkpdmisc) |2.1.1 | | |1 | +|Plasmidprofiler |0.1.6 | | | | +|plotKML |0.5-8 | | | | +|plotROC |2.2.0 | | | | +|pMineR |0.31 | | | | +|pmml |1.5.3 | | | | +|[pointblank](problems.md#pointblank) |0.1 | | |1 | +|politeness |0.1.2 | | | | +|pollstR |2.0.0 | | | | +|[polywog](problems.md#polywog) |0.4-0 | | |2 | +|postGIStools |0.2.1 | | | | +|powerbydesign |1.0.3 | | | | +|pre |0.4 | | | | +|predatory |1.2 | | | | +|[primerTree](problems.md#primertree) |1.0.3 | | |1 | +|[prisonbrief](problems.md#prisonbrief) |0.1.0 | | |1 | +|Prize |1.6.0 | | | | +|processmapR |0.2.1 | | | | +|[profr](problems.md#profr) |0.3.1 | | |2 | +|profvis |0.3.4 | | | | +|ProjectTemplate |0.8 | | | | +|promote |1.0.0 | | | | +|proPubBills |0.1 | | | | +|[proustr](problems.md#proustr) |0.2.1 | | |1 | +|prozor |0.2.3 | | | | +|pryr |0.1.3 | | | | +|psichomics |1.2.1 | | | | +|[psygenet2r](problems.md#psygenet2r) |1.9.1 |1 | |3 | +|[ptstem](problems.md#ptstem) |0.0.3 | | |1 | +|PubMedWordcloud |0.3.5 | | | | +|[pubprint](problems.md#pubprint) |0.2.1 | | |2 | +|[PWFSLSmoke](problems.md#pwfslsmoke) |0.99.33 | |1 | | +|[pxR](problems.md#pxr) |0.42.2 | |1 | | +|pxweb |0.6.3 | | | | +|QCAtools |0.2.3 | | | | +|qrcode |0.1.1 | | | | +|qualtRics |2.2 | | | | +|[quantoptr](problems.md#quantoptr) |0.1.2 | | |1 | +|[QuaternaryProd](problems.md#quaternaryprod) |1.4.0 | |1 |1 | +|[quipu](problems.md#quipu) |1.9.0 | | |1 | +|R2ucare |1.0.0 | | | | +|[radiant.model](problems.md#radiantmodel) |0.8.0 | | |1 | +|ragtop |0.5 | | | | +|randomcoloR |1.1.0 | | | | +|rapport |1.0 | | | | +|ratios |1.1.0 | | | | +|[rattle](problems.md#rattle) |5.1.0 |1 | | | +|[rAvis](problems.md#ravis) |0.1.4 | | |1 | +|[rcellminer](problems.md#rcellminer) |1.8.0 |2 |1 |3 | +|[rClinicalCodes](problems.md#rclinicalcodes) |1.0.1 | | |2 | +|rcrossref |0.8.0 | | | | +|[rcv](problems.md#rcv) |0.2.1 | | |2 | +|RDML |0.9-9 | | | | +|readJDX |0.2.3 | | | | +|[recoder](problems.md#recoder) |0.1 | | |1 | 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+|[SeqVarTools](problems.md#seqvartools) |1.14.0 | | |1 | +|[Seurat](problems.md#seurat) |2.1.0 | |1 | | +|sevenbridges |1.6.4 | | |-1 | +|[ShinyItemAnalysis](problems.md#shinyitemanalysis) |1.2.3 | | |1 | +|ShinyTester |0.1.0 | | | | +|[SICtools](problems.md#sictools) |1.6.0 | |1 |3 | +|[sidrar](problems.md#sidrar) |0.2.4 | | |1 | +|[sim1000G](problems.md#sim1000g) |1.33 | |1 | | +|simcausal |0.5.4 | | | | +|simPH |1.3.10 | | | | +|[simPop](problems.md#simpop) |1.0.0 | |1 |1 | +|simr |? | | | | +|[sincell](problems.md#sincell) |1.8.0 | |1 |2 | +|sjmisc |2.6.3 | | | | +|[skimr](problems.md#skimr) |1.0 | | |1 | +|smpic |0.1.0 | | | | +|snakecase |0.5.1 | | | | +|SnakeCharmR |1.0.7 | | | | +|snpReady |0.9.4 | | | | +|SocialMediaLab |0.23.2 | | | | +|[SomaticCancerAlterations](problems.md#somaticcanceralterations) |1.12.0 | | |2 | +|[sophisthse](problems.md#sophisthse) |0.7.0 | | |1 | +|[SoundexBR](problems.md#soundexbr) |1.2 | | |1 | +|spAddins |0.2.0 | | | | +|[spant](problems.md#spant) 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+|[sweep](problems.md#sweep) |0.2.0 | | |1 | +|sweidnumbr |1.4.1 | | | | +|swirl |2.4.3 | | | | +|[swirlify](problems.md#swirlify) |0.5.1 |1 | | | +|[syuzhet](problems.md#syuzhet) |1.0.4 | | |1 | +|tangram |0.3.2 | | | | +|[taRifx](problems.md#tarifx) |1.0.6 | | |3 | +|[taxa](problems.md#taxa) |0.2.0 | | |1 | +|taxize |0.9.0 | | | | +|[TBFmultinomial](problems.md#tbfmultinomial) |0.1.1 | |1 | | +|[TCGAbiolinks](problems.md#tcgabiolinks) |2.5.9 |1 -1 __+1__ |__+1__ |2 __+1__ | +|[TCGAbiolinksGUI](problems.md#tcgabiolinksgui) |1.2.1 | |1 |3 | +|TcGSA |0.10.5 | | | | +|templates |0.2.0 | | | | +|TexExamRandomizer |1.2.2 | | | | +|[text2vec](problems.md#text2vec) |0.5.0 | | |3 | +|textmineR |2.0.6 | | | | +|[textreuse](problems.md#textreuse) |0.1.4 | | |1 | +|tibbletime |0.0.2 | | | | +|tidycensus |0.3.1 | | | | +|[tidyquant](problems.md#tidyquant) |0.5.3 |1 |2 |1 | +|tidytext |0.1.5 | | | | +|[tidyverse](problems.md#tidyverse) |1.2.1 | | |1 | +|tigris |0.5.3 | | | | +|[tikzDevice](problems.md#tikzdevice) |0.10-1 | |1 | | +|timelineR |0.1.0 | | | | +|[timescape](problems.md#timescape) |1.0.0 | |1 |3 | +|[timetk](problems.md#timetk) |0.1.0 | | |1 | +|[TIN](problems.md#tin) |1.8.0 | | |1 | +|TLBC |1.0 | | | | +|tmlenet |0.1.0 | | | | +|[tmuxr](problems.md#tmuxr) |0.1.0 |1 | | | +|touch |0.1-3 | | | | +|[TPP](problems.md#tpp) |3.4.3 |1 | |3 | +|[tracktables](problems.md#tracktables) |1.10.0 | |1 |1 | +|[translateSPSS2R](problems.md#translatespss2r) |1.0.0 | | |1 | +|treeman |1.1.1 | | | | +|tropr |0.1.2 | | | | +|[tspmeta](problems.md#tspmeta) |1.2 | |1 | | +|TSTr |1.2 | | | | +|[tumblR](problems.md#tumblr) |1.1 | |1 |1 | +|uavRmp |0.5.1 | | | | +|[ucbthesis](problems.md#ucbthesis) |1.0 | | |1 | +|ukds |0.1.0 | | | | +|Uniquorn |1.4.2 | | | | +|unpivotr |0.3.0 | | | | +|uptasticsearch |0.1.0 | | | | +|urlshorteneR |0.9.2 | | | | +|[usmap](problems.md#usmap) |0.2.1 | | |3 | +|utilsIPEA |0.0.5 | | | | +|vagalumeR |0.1.1 | | | | +|[valaddin](problems.md#valaddin) |0.1.2 | | |1 | +|validaRA |0.1.1 | | | | +|valr |0.3.1 | | | | +|[vardpoor](problems.md#vardpoor) |0.9.11 |1 |1 | | +|[VarfromPDB](problems.md#varfrompdb) |2.2.7 | |1 | | +|vcfR |1.6.0 | | | | +|[VDAP](problems.md#vdap) |2.0.0 | |1 | | +|vembedr |0.1.3 | | | | +|vennplot |1.0 | | | | +|[vetools](problems.md#vetools) |1.3-28 | | |1 | +|vfcp |1.4.0 | | | | +|ViSiElse |1.2.0 | | | | +|vkR |0.1 | | | | +|vortexR |1.1.4 | | | | +|[vows](problems.md#vows) |0.5 | |1 | | +|[vqtl](problems.md#vqtl) |1.2.0 | | |1 | +|[wavClusteR](problems.md#wavcluster) |2.10.0 | |1 |3 | +|webchem |0.3.0 | | | | +|webTRISr |0.1.0 | | | | +|[wikilake](problems.md#wikilake) |0.3 | | |1 | +|wikipediatrend |1.1.14 | | | | +|WikiSocio |0.7.0 | | | | +|[wingui](problems.md#wingui) |0.2 | |1 | | +|[wordbankr](problems.md#wordbankr) |0.2.0 | |1 |1 | +|[wsrf](problems.md#wsrf) |1.7.17 | |1 | | +|[wux](problems.md#wux) |2.2-1 | |1 | | +|x.ent |1.1.7 | | | | +|x12 |1.9.0 | | | | +|[x12GUI](problems.md#x12gui) |0.13.0 |1 | | | +|xesreadR |0.2.2 | | | | +|Xplortext |1.1.0 | | | | +|[xpose](problems.md#xpose) |0.4.0 |1 | |1 | +|yhatr |0.15.1 | | | | +|[ztype](problems.md#ztype) |0.1.0 | | |1 | diff --git a/revdep/problems.md b/revdep/problems.md index 4711f629..49222bf4 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -39,6 +39,13 @@ Version: 0.18-0 ## In both +* checking whether package ‘afex’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘lme4’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/afex/new/afex.Rcheck/00install.out’ for details. + ``` + * checking Rd cross-references ... NOTE ``` Packages unavailable to check Rd xrefs: ‘ez’, ‘ascii’ @@ -111,6 +118,38 @@ Version: 0.1.0 All declared Imports should be used. ``` +# alpine + +Version: 1.2.0 + +## Newly broken + +* checking examples ... ERROR + ``` + ... + > library(rtracklayer) + > gap <- ERR188088() + snapshotDate(): 2016-10-01 + see ?alpineData and browseVignettes('alpineData') for documentation + loading from cache ‘/Users/hadley//.ExperimentHub/167’ + > dir <- system.file(package="alpineData", "extdata") + > bam.file <- c("ERR188088" = file.path(dir,"ERR188088.bam")) + > export(gap, con=bam.file) + > + > data(preprocessedData) + > + > w <- getFragmentWidths(bam.file, ebt.fit[[2]]) + Warning in doTryCatch(return(expr), name, parentenv, handler) : + [bam_header_read] EOF marker is absent. The input is probably truncated. + Warning in doTryCatch(return(expr), name, parentenv, handler) : + [bam_header_read] invalid BAM binary header (this is not a BAM file). + Error in value[[3L]](cond) : + failed to open BamFile: SAM/BAM header missing or empty + file: '/Users/hadley/Documents/tidyverse/stringr/revdep/library.noindex/alpine/alpineData/extdata/ERR188088.bam' + Calls: getFragmentWidths ... tryCatch -> tryCatchList -> tryCatchOne -> + Execution halted + ``` + # AmostraBrasil Version: 1.2 @@ -191,6 +230,13 @@ Version: 1.0.0 ## In both +* checking whether package ‘banocc’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘rstan’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/banocc/new/banocc.Rcheck/00install.out’ for details. + ``` + * checking R code for possible problems ... NOTE ``` calc_snc: no visible global function definition for ‘sd’ @@ -242,6 +288,7 @@ Version: 1.0.1 * checking whether package ‘basecallQC’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘knitr’ was built under R version 3.4.3 Warning: package ‘yaml’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/basecallQC/new/basecallQC.Rcheck/00install.out’ for details. ``` @@ -360,6 +407,7 @@ Version: 1.4.0 ``` Found the following significant warnings: Warning: package ‘cgdsr’ was built under R version 3.4.3 + Warning: package ‘RCurl’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/bioCancer/new/bioCancer.Rcheck/00install.out’ for details. ``` @@ -453,7 +501,7 @@ Version: 0.3.1 }(28L, "", TRUE) ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 68 SKIPPED: 0 FAILED: 1 + OK: 69 SKIPPED: 0 FAILED: 1 1. Error: download.file.custom is.dir (@test_utils.R#138) Error: testthat unit tests failed @@ -464,33 +512,7 @@ Version: 0.3.1 Version: 0.5.2 -## In both - -* checking examples ... ERROR - ``` - ... - > ### Name: getDatasets - > ### Title: Retrieve All Available Datasets for a BioMart Database - > ### Aliases: getDatasets - > - > ### ** Examples - > - > # search for available datasets - > getMarts() - Opening and ending tag mismatch: link line 7 and head - Opening and ending tag mismatch: link line 6 and html - Premature end of data in tag link line 5 - Premature end of data in tag base line 3 - Premature end of data in tag head line 2 - Premature end of data in tag html line 1 - Error: 1: Opening and ending tag mismatch: link line 7 and head - 2: Opening and ending tag mismatch: link line 6 and html - 3: Premature end of data in tag link line 5 - 4: Premature end of data in tag base line 3 - 5: Premature end of data in tag head line 2 - 6: Premature end of data in tag html line 1 - Execution halted - ``` +## Newly fixed * checking tests ... ``` @@ -498,31 +520,31 @@ Version: 0.5.2 Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt' - Content type 'unknown' length 2242553 bytes (2.1 MB) + Content type 'unknown' length 2243299 bytes (2.1 MB) ================================================== trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt' - Content type 'unknown' length 3045016 bytes (2.9 MB) + Content type 'unknown' length 3047611 bytes (2.9 MB) ================================================== trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/assembly_summary.txt' - Content type 'unknown' length 389585 bytes (380 KB) + Content type 'unknown' length 666851 bytes (651 KB) ================================================== ══ testthat results ═══════════════════════════════════════════════════════════ OK: 5 SKIPPED: 60 FAILED: 1 - 1. Error: The biomart() interface works properly.. (@test-biomart.R#10) + 1. Error: The biomart() interface works properly.. (@test-biomart.R#14) Error: testthat unit tests failed Execution halted ``` +## In both + * checking re-building of vignette outputs ... WARNING ``` Error in re-building vignettes: ... - Quitting from lines 42-51 (Functional_Annotation.Rmd) + Quitting from lines 97-112 (Functional_Annotation.Rmd) Error: processing vignette 'Functional_Annotation.Rmd' failed with diagnostics: - Unexpected format to the list of available marts. - Please check the following URL manually, and try ?listMarts for advice. - http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt + The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. Execution halted ``` @@ -592,26 +614,6 @@ Version: 1.0.0 ## In both -* checking examples ... ERROR - ``` - Running examples in ‘branchpointer-Ex.R’ failed - The error most likely occurred in: - - > ### Name: snpToQuery - > ### Title: Gets a branchpointer formatted query from refsnp ids - > ### Aliases: snpToQuery - > - > ### ** Examples - > - > mart.snp <- biomaRt::useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host="www.ensembl.org") - Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, : - Unexpected format to the list of available marts. - Please check the following URL manually, and try ?listMarts for advice. - http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt - Calls: -> listMarts - Execution halted - ``` - * checking whether package ‘branchpointer’ can be installed ... WARNING ``` Found the following significant warnings: @@ -619,32 +621,6 @@ Version: 1.0.0 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/branchpointer/new/branchpointer.Rcheck/00install.out’ for details. ``` -* checking re-building of vignette outputs ... WARNING - ``` - ... - Loading required package: GenomeInfoDb - Loading required package: GenomicRanges - Loading required package: Biostrings - Loading required package: XVector - - Attaching package: 'Biostrings' - - The following object is masked from 'package:base': - - strsplit - - Loading required package: rtracklayer - Loading required package: caret - Loading required package: lattice - Loading required package: ggplot2 - Quitting from lines 210-213 (branchpointer.Rnw) - Error: processing vignette 'branchpointer.Rnw' failed with diagnostics: - Unexpected format to the list of available marts. - Please check the following URL manually, and try ?listMarts for advice. - http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt - Execution halted - ``` - # breathtestcore Version: 0.4.0 @@ -713,6 +689,7 @@ Version: 4.2-0 * checking whether package ‘Causata’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘RCurl’ was built under R version 3.4.3 Warning: package ‘foreach’ was built under R version 3.4.3 Warning: package ‘doMC’ was built under R version 3.4.3 Warning: package ‘iterators’ was built under R version 3.4.3 @@ -873,9 +850,9 @@ Version: 1.4.0 * checking installed package size ... NOTE ``` - installed size is 18.4Mb + installed size is 18.7Mb sub-directories of 1Mb or more: - data 17.7Mb + data 18.0Mb ``` * checking R code for possible problems ... NOTE @@ -892,6 +869,19 @@ Version: 1.4.0 ID chrom dataMatrix midpoint name stain ``` +# CLME + +Version: 2.0-8 + +## In both + +* checking whether package ‘CLME’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘lme4’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/CLME/new/CLME.Rcheck/00install.out’ for details. + ``` + # compcodeR Version: 1.12.0 @@ -938,7 +928,7 @@ Version: 1.12.0 # configr -Version: 0.3.1.1 +Version: 0.3.2 ## In both @@ -1224,7 +1214,7 @@ Version: 1.16.0 + splice_matrix=FALSE, COSMIC=FALSE) Build TranscriptDB object (txdb.sqlite) ... Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : - 'names' attribute [211] must be the same length as the vector [209] + 'names' attribute [212] must be the same length as the vector [210] Calls: PrepareAnnotationRefseq ... trackNames -> .local -> ucscTracks -> ucscTracks -> .local Execution halted ``` @@ -1291,7 +1281,7 @@ Version: 1.16.0 Error: processing vignette 'customProDB.Rnw' failed with diagnostics: chunk 1 (label = dbSNPversion) Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : - 'names' attribute [211] must be the same length as the vector [209] + 'names' attribute [212] must be the same length as the vector [210] Execution halted ``` @@ -1454,6 +1444,13 @@ Version: 1.2.10 * R CMD check timed out +* checking whether package ‘DeepBlueR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘RCurl’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/DeepBlueR/new/DeepBlueR.Rcheck/00install.out’ for details. + ``` + # DeLorean Version: 1.2.5 @@ -1662,6 +1659,7 @@ Version: 1.1.0 ``` Error in re-building vignettes: ... + Warning: package 'knitr' was built under R version 3.4.3 Loading required package: ggplot2 Quitting from lines 172-181 (intro.Rmd) Error: processing vignette 'intro.Rmd' failed with diagnostics: @@ -1679,6 +1677,7 @@ Version: 2.1 * checking whether package ‘eiCompare’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 Warning: package ‘msm’ was built under R version 3.4.3 Warning: package ‘foreach’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/eiCompare/new/eiCompare.Rcheck/00install.out’ for details. @@ -1866,7 +1865,7 @@ Version: 1.0.0 expand Warning in in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, : - You changed the working directory to /private/tmp/Rtmpekf1iu (probably via setwd()). It will be restored to /Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/EventPointer/new/EventPointer.Rcheck/vign_test/EventPointer/vignettes. See the Note section in ?knitr::knit + You changed the working directory to /private/tmp/RtmpdZPWKr (probably via setwd()). It will be restored to /Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/EventPointer/new/EventPointer.Rcheck/vign_test/EventPointer/vignettes. See the Note section in ?knitr::knit Error: processing vignette 'EventPointer.Rmd' failed with diagnostics: path for html_dependency not found: Execution halted @@ -2006,32 +2005,17 @@ Version: 2.0 contains 'methods'). ``` -# FedData +# fergm -Version: 2.5.0 +Version: 0.2.1 -## Newly broken +## In both -* checking tests ... +* checking whether package ‘fergm’ can be installed ... WARNING ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - > test_check("FedData") - ── 1. Error: ITRDB version files are available (@test.ITRDB.R#23) ───────────── - Got a 530 ftp-server response when 220 was expected - 1: readLines(curl::curl(url, handle = hand)) at testthat/test.ITRDB.R:23 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 27 SKIPPED: 0 FAILED: 1 - 1. Error: ITRDB version files are available (@test.ITRDB.R#23) - - Error: testthat unit tests failed - In addition: Warning messages: - 1: closing unused connection 3 (ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/) - 2: closing unused connection 4 (http://websoilsurvey.sc.egov.usda.gov/DSD/Download/Cache/SSA/blah.zip) - 3: closing unused connection 3 (https://websoilsurvey.sc.egov.usda.gov/DSD/Download/Cache/SSA/wss_SSA_CO670_[2017-09-06].zip) - Execution halted + Found the following significant warnings: + Warning: package ‘rstan’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/fergm/new/fergm.Rcheck/00install.out’ for details. ``` # FFTrees @@ -2074,13 +2058,6 @@ Version: 0.3.0 Package suggested but not available for checking: ‘fivethirtyeight’ ``` -* checking installed package size ... NOTE - ``` - installed size is 5.3Mb - sub-directories of 1Mb or more: - data 4.5Mb - ``` - * checking data for non-ASCII characters ... NOTE ``` Note: found 371 marked UTF-8 strings @@ -2253,6 +2230,19 @@ Version: 0.1.0 All declared Imports should be used. ``` +# frequencyConnectedness + +Version: 0.1.6 + +## In both + +* checking whether package ‘frequencyConnectedness’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/frequencyConnectedness/new/frequencyConnectedness.Rcheck/00install.out’ for details. + ``` + # FRESA.CAD Version: 2.2.1 @@ -2331,6 +2321,13 @@ Version: 1.1.2 ## In both +* checking whether package ‘games’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/games/new/games.Rcheck/00install.out’ for details. + ``` + * checking R code for possible problems ... NOTE ``` ... @@ -2408,6 +2405,24 @@ Version: 0.2.6 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/GenomicTools/new/GenomicTools.Rcheck/00install.out’ for details. ``` +# GetITRData + +Version: 0.6 + +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Quitting from lines 100-113 (gitrd-vignette-introduction.Rmd) + Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics: + Zipped file contains 0 files. This is likelly a problem with the downloaded file. Try running the code again as the corrupted zip file was deleted and will be downloaded again. + + If the problem persists, my suggestions is to remove the time period with problem. + Execution halted + ``` + # ggenealogy Version: 0.3.0 @@ -2493,7 +2508,7 @@ Version: 1.0 Version: 1.10.0 -## In both +## Newly fixed * checking installed package size ... NOTE ``` @@ -2502,6 +2517,8 @@ Version: 1.10.0 data 4.3Mb ``` +## In both + * checking R code for possible problems ... NOTE ``` GO_analyse: no visible binding for global variable ‘microarray2dataset’ @@ -2580,6 +2597,7 @@ Version: 0.1 ``` Found the following significant warnings: Warning: package ‘msm’ was built under R version 3.4.3 + Warning: package ‘MASS’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/GUIgems/new/GUIgems.Rcheck/00install.out’ for details. ``` @@ -2667,7 +2685,7 @@ Version: 0.3.2 # htmlTable -Version: 1.11.0 +Version: 1.11.1 ## In both @@ -2872,6 +2890,85 @@ ERROR: lazy loading failed for package ‘HydeNet’ ** testing if installed package can be loaded * DONE (HydeNet) +``` +# hydroscoper + +Version: 0.1.0 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 474 marked UTF-8 strings + ``` + +# IATscores + +Version: 0.1-2 + +## Newly broken + +* checking whether package ‘IATscores’ can be installed ... ERROR + ``` + Installation failed. + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/IATscores/new/IATscores.Rcheck/00install.out’ for details. + ``` + +## Newly fixed + +* checking R code for possible problems ... NOTE + ``` + ... + Gscores: no visible global function definition for ‘filter’ + MiniDscores: no visible global function definition for ‘filter’ + MiniDscores: no visible global function definition for ‘object.size’ + RobustScores: no visible global function definition for ‘filter’ + SplitHalf: no visible global function definition for ‘cor’ + TestRetest: no visible global function definition for ‘filter’ + TestRetest: no visible global function definition for ‘cor’ + WPRscores: no visible global function definition for ‘filter’ + WPRscores: no visible global function definition for ‘quantile’ + WPRscores: no visible global function definition for ‘sd’ + computeMinid: no visible global function definition for ‘sd’ + doP1P2: no visible global function definition for ‘filter’ + doP1P2: no visible global function definition for ‘sd’ + doP1P2P3P4: no visible global function definition for ‘filter’ + specialvar: no visible global function definition for ‘var’ + Undefined global functions or variables: + cor filter object.size quantile sd var + Consider adding + importFrom("stats", "cor", "filter", "quantile", "sd", "var") + importFrom("utils", "object.size") + to your NAMESPACE file. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘IATscores’ ... +** package ‘IATscores’ successfully unpacked and MD5 sums checked +** R +** preparing package for lazy loading +Error : object ‘str_join’ is not exported by 'namespace:stringr' +ERROR: lazy loading failed for package ‘IATscores’ +* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/IATscores/new/IATscores.Rcheck/IATscores’ + +``` +### CRAN + +``` +* installing *source* package ‘IATscores’ ... +** package ‘IATscores’ successfully unpacked and MD5 sums checked +** R +** preparing package for lazy loading +** help +*** installing help indices +** building package indices +** testing if installed package can be loaded +* DONE (IATscores) + ``` # icd @@ -2899,9 +2996,6 @@ Version: 1.0.0 ## In both -* R CMD check timed out - - * checking for hidden files and directories ... NOTE ``` Found the following hidden files and directories: @@ -2919,89 +3013,6 @@ Version: 1.0.0 airway ideal_env ``` -# imager - -Version: 0.40.2 - -## In both - -* checking whether package ‘imager’ can be installed ... ERROR - ``` - Installation failed. - See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/imager/new/imager.Rcheck/00install.out’ for details. - ``` - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘spatstat’ - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘imager’ ... -** package ‘imager’ successfully unpacked and MD5 sums checked -checking for gcc... gcc -checking whether the C compiler works... yes -checking for C compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether we are using the GNU C compiler... yes -checking whether gcc accepts -g... yes -checking for gcc option to accept ISO C89... none needed -checking how to run the C preprocessor... gcc -E -checking for X... libraries /usr/X11/lib, headers /usr/X11/include -configure: Checking if FFTW3 library is available using pkg-config -checking for pkg-config... /usr/local/bin/pkg-config -checking pkg-config is at least version 0.9.0... yes -checking for FFTW... no -FFTW library not found, please install fftw3 for better FFT support. -checking for TIFFOpen in -ltiff... yes -configure: creating ./config.status -config.status: creating src/Makevars -** libs -ccache clang++ -Qunused-arguments -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/X11/include -Dcimg_use_tiff -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' -I"/Users/hadley/Documents/tidyverse/stringr/revdep/library.noindex/imager/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang: error: unsupported option '-fopenmp' -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘imager’ -* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/imager/new/imager.Rcheck/imager’ - -``` -### CRAN - -``` -* installing *source* package ‘imager’ ... -** package ‘imager’ successfully unpacked and MD5 sums checked -checking for gcc... gcc -checking whether the C compiler works... yes -checking for C compiler default output file name... a.out -checking for suffix of executables... -checking whether we are cross compiling... no -checking for suffix of object files... o -checking whether we are using the GNU C compiler... yes -checking whether gcc accepts -g... yes -checking for gcc option to accept ISO C89... none needed -checking how to run the C preprocessor... gcc -E -checking for X... libraries /usr/X11/lib, headers /usr/X11/include -configure: Checking if FFTW3 library is available using pkg-config -checking for pkg-config... /usr/local/bin/pkg-config -checking pkg-config is at least version 0.9.0... yes -checking for FFTW... no -FFTW library not found, please install fftw3 for better FFT support. -checking for TIFFOpen in -ltiff... yes -configure: creating ./config.status -config.status: creating src/Makevars -** libs -ccache clang++ -Qunused-arguments -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -fopenmp -I/usr/X11/include -Dcimg_use_tiff -I../inst/include -DCIMG_COMPILING -Dcimg_use_rng -Dcimg_use_r -Dcimg_use_fftw3_singlethread -Dcimg_verbosity=1 -Dcimg_date='""' -Dcimg_time='""' -I"/Users/hadley/Documents/tidyverse/stringr/revdep/library.noindex/imager/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang: error: unsupported option '-fopenmp' -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘imager’ -* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/imager/old/imager.Rcheck/imager’ - -``` # IONiseR Version: 2.0.0 @@ -3068,30 +3079,12 @@ Version: 2.0.0 time_group x y zvalue ``` -# ISOweek - -Version: 0.6-2 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘surveillance’ - ``` - # jpmesh Version: 1.0.1 ## In both -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - R 4.6Mb - ``` - * checking dependencies in R code ... NOTE ``` Namespace in Imports field not imported from: ‘readr’ @@ -3169,7 +3162,7 @@ Version: 0.6.1 # knitr -Version: 1.17 +Version: 1.18 ## Newly broken @@ -3451,6 +3444,7 @@ Version: 1.2.1 Error in re-building vignettes: ... Warning: package 'reshape2' was built under R version 3.4.3 + Warning: package 'knitr' was built under R version 3.4.3 Warning: package 'registry' was built under R version 3.4.3 Warning: package 'rsvd' was built under R version 3.4.3 Quitting from lines 90-102 (MAITAnalysis.Rmd) @@ -3504,9 +3498,8 @@ Version: 1.8.1 * checking installed package size ... NOTE ``` - installed size is 8.8Mb + installed size is 8.7Mb sub-directories of 1Mb or more: - data 1.0Mb extdata 6.7Mb ``` @@ -4170,9 +4163,6 @@ Version: 1.10.0 ## In both -* R CMD check timed out - - * checking R code for possible problems ... NOTE ``` combinePvalues: no visible global function definition for ‘pnorm’ @@ -4202,6 +4192,8 @@ Version: 1.1.0 * checking whether package ‘nauf’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘lme4’ was built under R version 3.4.3 + Warning: package ‘rstanarm’ was built under R version 3.4.3 Warning: package ‘Rcpp’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/nauf/new/nauf.Rcheck/00install.out’ for details. ``` @@ -4219,9 +4211,9 @@ Version: 0.99.2 * checking installed package size ... NOTE ``` - installed size is 8.5Mb + installed size is 8.6Mb sub-directories of 1Mb or more: - data 8.1Mb + data 8.2Mb ``` # Nippon @@ -4398,32 +4390,31 @@ Version: 1.1.0 Version: 1.6.0 -## Newly fixed - -* R CMD check timed out - - ## In both * checking examples ... ERROR ``` - Running examples in ‘PGA-Ex.R’ failed - The error most likely occurred in: + ... - > ### Name: PrepareAnnotationEnsembl2 - > ### Title: Prepare annotation from ENSEMBL - > ### Aliases: PrepareAnnotationEnsembl2 + > ### Name: PrepareAnnotationRefseq2 + > ### Title: Prepare annotation from Refseq + > ### Aliases: PrepareAnnotationRefseq2 > > ### ** Examples > - > ensembl <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", - + host="grch37.ensembl.org", path="/biomart/martservice", - + archive=FALSE) - Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, : - Unexpected format to the list of available marts. - Please check the following URL manually, and try ?listMarts for advice. - http://grch37.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt - Calls: -> listMarts + > transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499") + > pepfasta <- system.file("extdata", "refseq_pro_seq.fasta", + + package="customProDB") + > CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta", + + package="customProDB") + > annotation_path <- tempdir() + > PrepareAnnotationRefseq2(genome='hg19', CDSfasta, pepfasta, annotation_path, + + dbsnp=NULL, transcript_ids=transcript_ids, + + splice_matrix=FALSE, COSMIC=FALSE) + Build TranscriptDB object (txdb.sqlite) ... + Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : + 'names' attribute [212] must be the same length as the vector [210] + Calls: PrepareAnnotationRefseq2 ... trackNames -> .local -> ucscTracks -> ucscTracks -> .local Execution halted ``` @@ -4668,17 +4659,8 @@ Version: 1.9.1 ## In both -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in engine$weave(file, quiet = quiet, encoding = enc) : - The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. - Quitting from lines 2-32 (case_study.Rmd) - Error: processing vignette 'case_study.Rmd' failed with diagnostics: - could not find function "doc_date" - Execution halted - ``` +* R CMD check timed out + * checking installed package size ... NOTE ``` @@ -5036,6 +5018,13 @@ Version: 0.2.1 ## In both +* checking installed package size ... NOTE + ``` + installed size is 5.2Mb + sub-directories of 1Mb or more: + data 5.0Mb + ``` + * checking data for non-ASCII characters ... NOTE ``` Note: found 6543 marked UTF-8 strings @@ -5132,6 +5121,19 @@ Version: 1.0 to your NAMESPACE file. ``` +# RGENERATEPREC + +Version: 1.2 + +## In both + +* checking whether package ‘RGENERATEPREC’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/RGENERATEPREC/new/RGENERATEPREC.Rcheck/00install.out’ for details. + ``` + # rmarkdown Version: 1.8 @@ -5155,6 +5157,7 @@ Version: 1.4 ``` Found the following significant warnings: Warning: package ‘irtoys’ was built under R version 3.4.3 + Warning: package ‘MASS’ was built under R version 3.4.3 Warning: package ‘msm’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/RndTexExams/new/RndTexExams.Rcheck/00install.out’ for details. ``` @@ -5217,6 +5220,26 @@ Version: 1.10.0 ## In both +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Warning in block_exec(params) : + failed to tidy R code in chunk + reason: Error in loadNamespace(name) : there is no package called 'formatR' + + Warning in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : + URL https://ftp.ncbi.nlm.nih.gov/geo/series/GSE4nnn/GSE4158/matrix//geo/series/GSE4nnn/GSE4158/: cannot open destfile '/tmp/RtmpmAg0LG//geo/series/GSE4nnn/GSE4158/', reason 'No such file or directory' + Warning in download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s", : + download had nonzero exit status + Warning in file(con, "r") : + cannot open file '/tmp/RtmpmAg0LG//geo/series/GSE4nnn/GSE4158/': No such file or directory + Quitting from lines 90-114 (Rnits-vignette.Rnw) + Error: processing vignette 'Rnits-vignette.Rnw' failed with diagnostics: + cannot open the connection + Execution halted + ``` + * checking DESCRIPTION meta-information ... NOTE ``` Malformed Description field: should contain one or more complete sentences. @@ -5549,6 +5572,19 @@ Version: 0.2.4 All declared Imports should be used. ``` +# sim1000G + +Version: 1.33 + +## In both + +* checking whether package ‘sim1000G’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/sim1000G/new/sim1000G.Rcheck/00install.out’ for details. + ``` + # simPop Version: 1.0.0 @@ -5641,6 +5677,18 @@ Version: 1.8.0 See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. ``` +# skimr + +Version: 1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘knitr’ + All declared Imports should be used. + ``` + # SomaticCancerAlterations Version: 1.12.0 @@ -5943,7 +5991,7 @@ Version: 1.0.4 ``` installed size is 5.6Mb sub-directories of 1Mb or more: - R 1.9Mb + R 1.8Mb extdata 3.1Mb ``` @@ -6022,33 +6070,7 @@ Version: 0.1.1 Version: 2.5.9 -## In both - -* checking examples ... ERROR - ``` - ... - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - |NA |NA |NA |NA | - Error in checkProjectInput(project) : - Please set a valid project argument from the column id above. Project TCGA-ACC was not found. - Calls: GDCquery -> checkProjectInput - Execution halted - ``` +## Newly broken * checking tests ... ``` @@ -6098,6 +6120,44 @@ Version: 2.5.9 Execution halted ``` +* checking for unstated dependencies in vignettes ... NOTE + ``` + 'library' or 'require' call not declared from: ‘DT’ + ``` + +## Newly fixed + +* R CMD check timed out + + +## In both + +* checking examples ... ERROR + ``` + ... + |NA |NA |NA |NA | + |Thymic Epithelial Neoplasms |Neuroepitheliomatous Neoplasms |Basal Cell Neoplasms |Ductal and Lobular Neoplasms | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + |NA |NA |NA |NA | + Error in checkProjectInput(project) : + Please set a valid project argument from the column id above. Project TCGA-ACC was not found. + Calls: GDCquery -> checkProjectInput + Execution halted + ``` + * checking installed package size ... NOTE ``` installed size is 61.0Mb @@ -6133,11 +6193,6 @@ Version: 2.5.9 visNet ``` -* checking for unstated dependencies in vignettes ... NOTE - ``` - 'library' or 'require' call not declared from: ‘DT’ - ``` - # TCGAbiolinksGUI Version: 1.2.1 @@ -6542,12 +6597,32 @@ Version: 1.0.0 to your NAMESPACE file. ``` +# tspmeta + +Version: 1.2 + +## In both + +* checking whether package ‘tspmeta’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/tspmeta/new/tspmeta.Rcheck/00install.out’ for details. + ``` + # tumblR Version: 1.1 ## In both +* checking whether package ‘tumblR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘RCurl’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/tumblR/new/tumblR.Rcheck/00install.out’ for details. + ``` + * checking R code for possible problems ... NOTE ``` http.connection: no visible global function definition for ‘setNames’ @@ -6642,6 +6717,13 @@ Version: 0.9.11 Execution halted ``` +* checking whether package ‘vardpoor’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/vardpoor/new/vardpoor.Rcheck/00install.out’ for details. + ``` + # VarfromPDB Version: 2.2.7 @@ -6655,6 +6737,19 @@ Version: 2.2.7 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/VarfromPDB/new/VarfromPDB.Rcheck/00install.out’ for details. ``` +# VDAP + +Version: 2.0.0 + +## In both + +* checking whether package ‘VDAP’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘MASS’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/VDAP/new/VDAP.Rcheck/00install.out’ for details. + ``` + # vetools Version: 1.3-28 @@ -6687,6 +6782,19 @@ Version: 1.3-28 contains 'methods'). ``` +# vows + +Version: 0.5 + +## In both + +* checking whether package ‘vows’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘lme4’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/vows/new/vows.Rcheck/00install.out’ for details. + ``` + # vqtl Version: 1.2.0 @@ -6821,6 +6929,7 @@ Version: 2.2-1 * checking whether package ‘wux’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘spam’ was built under R version 3.4.3 Warning: package ‘dotCall64’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/wux/new/wux.Rcheck/00install.out’ for details. ``` @@ -6843,32 +6952,30 @@ Version: 0.13.0 Version: 0.4.0 -## Newly broken +## In both * checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - ...) - 8: all.equal.tbl_df(target[[i]], current[[i]], check.attributes = check.attributes, - use.names = use.names, ...) 9: equal_data_frame(target, current, ignore_col_order = ignore_col_order, ignore_row_order = ignore_row_order, convert = convert) ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 525 SKIPPED: 0 FAILED: 4 - 1. Failure: summary is properly created with the appropriate information (@test-model-summary.R#43) - 2. Failure: Termination messages are parsed when minimization is terminated (@test-model-summary.R#108) - 3. Error: properly creates the xpdb when using the file argument (@test-xpose_data.R#39) - 4. Error: properly creates the xpdb when using the runno argument (@test-xpose_data.R#52) + OK: 522 SKIPPED: 0 FAILED: 7 + 1. Failure: Check list_data returns a proper message (@test-console_outputs.R#43) + 2. Failure: Check list_files returns a proper message (@test-console_outputs.R#47) + 3. Failure: Check list_special returns a proper message (@test-console_outputs.R#51) + 4. Failure: summary is properly created with the appropriate information (@test-model-summary.R#43) + 5. Failure: Termination messages are parsed when minimization is terminated (@test-model-summary.R#108) + 6. Error: properly creates the xpdb when using the file argument (@test-xpose_data.R#39) + 7. Error: properly creates the xpdb when using the runno argument (@test-xpose_data.R#52) Error: testthat unit tests failed Execution halted ``` -## In both - * checking dependencies in R code ... NOTE ``` Namespace in Imports field not imported from: ‘gridExtra’