diff --git a/DESCRIPTION b/DESCRIPTION index bfc2d974..f25e0e9d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: stringr Title: Simple, Consistent Wrappers for Common String Operations -Version: 1.2.0.9000 +Version: 1.3.0 Authors@R: c( person("Hadley", "Wickham", , "hadley@rstudio.com", c("aut", "cre", "cph")), person("RStudio", role = c("cph", "fnd")) diff --git a/cran-comments.md b/cran-comments.md index 95b9bfb6..f9bfef39 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -10,31 +10,52 @@ ## revdepcheck results -We checked 573 reverse dependencies (510 from CRAN + 63 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 612 reverse dependencies (551 from CRAN + 61 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package. - * We saw 1 new problems - * We failed to check 10 packages + * We saw 4 new problems + * We failed to check 9 packages Issues with CRAN packages are summarised below. ### New problems (This reports the first line of each new failure) -* alphavantager - checking tests ... +* banR + checking re-building of vignette outputs ... WARNING - This appears to be a web test that is failing because the server is - down. + Unrelated to stringr, error is "The API sent back an error 502" + +* RSMET + checking examples ... ERROR + + Unrelated to stringr, error is + Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France" + +* stormwindmodel + checking re-building of vignette outputs ... WARNING + + Unrelated to stringr, error is: + Warning: geocode failed with status OVER_QUERY_LIMIT, location = "georgia" + +* vardpoor + checking examples ... ERROR + + Seems unrelated to stringr. Error is: + Error in gsd(employed, na.rm = TRUE) : + negative length vectors are not allowed + Calls: vardannual -> vardcros -> [ -> [.data.table -> gforce -> gsd + + I did not see this error when I last ran the checks, but I have + notified the author today. ### Failed to check -* ALA4R (check timed out) -* aslib (failed to install) -* blastula (failed to install) -* bridgesampling (check timed out) -* CollapsABEL (failed to install) -* dtree (failed to install) -* ggmap (failed to install) -* GSIF (failed to install) -* heemod (failed to install) -* taRifx (failed to install) +* CoFRA (NA) +* dynamichazard (failed to install) +* EasyMARK (failed to install) +* fastLink (failed to install) +* FRESA.CAD (failed to install) +* IATscores (failed to install) +* imager (failed to install) +* morse (failed to install) +* rsunlight (failed to install) diff --git a/revdep/README.md b/revdep/README.md index be97378d..80c4f915 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -9,7 +9,7 @@ |language |(EN) | |collate |en_US.UTF-8 | |tz |America/Chicago | -|date |2017-12-29 | +|date |2018-01-29 | # Dependencies @@ -22,643 +22,652 @@ # Revdeps -## Couldn't check (23) +## Couldn't check (16) |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 |1 | | +|CoFRA |? | | | | +|[customProDB](problems.md#customprodb) |1.16.0 |1 | |3 | +|[DeepBlueR](problems.md#deepbluer) |1.2.10 |2 | | | |[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 | | | +|[fastLink](problems.md#fastlink) |0.3.0 |1 | | | |[FRESA.CAD](problems.md#fresacad) |2.2.1 |1 | | | -|[HydeNet](problems.md#hydenet) |0.10.6 |-2 __+1__ |-1 | | |[IATscores](problems.md#iatscores) |0.1-2 |__+1__ | |-1 | -|imager |? | | | | -|ISOweek |? | | | | -|[monocle](problems.md#monocle) |2.4.0 |__+1__ |-1 |-1 | +|[imager](problems.md#imager) |0.40.2 |1 | |1 | +|[monocle](problems.md#monocle) |2.4.0 |-1 __+1__ |-1 |-1 | |[morse](problems.md#morse) |2.2.0 |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 |? | | | | +|TCGAbiolinksGUI |? | | | | |[TPP](problems.md#tpp) |3.4.3 |1 | |3 | -## Broken (5) +## Broken (6) -|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__ | +|package |version |error |warning |note | +|:--------------------------------------------|:-------|:------|:-------|:----| +|[alpine](problems.md#alpine) |1.2.0 |__+1__ | | | +|[banR](problems.md#banr) |0.2.0 | |__+1__ |1 | +|[RSMET](problems.md#rsmet) |1.2.9 |__+1__ | | | +|[sincell](problems.md#sincell) |1.8.0 | |__+1__ |2 | +|[stormwindmodel](problems.md#stormwindmodel) |0.1.0 | |__+1__ | | +|[vardpoor](problems.md#vardpoor) |0.9.11 |__+1__ |1 | | -## All (597) +## All (612) -|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 | -|[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](problems.md#rgenerateprec) |1.2 | |1 | | -|rgeopat2 |0.1.4 | | | | -|Rilostat |0.2 | | | | -|RJafroc |0.1.1 | | | | -|RLogicalOps |0.1 | | | | -|[rmarkdown](problems.md#rmarkdown) |1.8 | | |1 | -|rmonad |? | | | | -|[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 | |1 |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](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) |0.6.0 | |1 |1 | -|spatsurv |1.1 | | | | -|spectacles |0.5-0 | | | | -|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 | | | | -|swatches |0.5.0 | | | | -|[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 |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 | +|package |version |error |warning |note | +|:----------------------------------------------------------------|:---------|:---------|:-------|:----| +|abcrf |1.7 | | | | +|[abjutils](problems.md#abjutils) |0.2.1 | | |1 | +|acs |2.1.2 | | | | +|aemo |0.2.0 | | | | +|[afex](problems.md#afex) |0.19-1 | |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 | +|[annovarR](problems.md#annovarr) |1.0.0 |1 | | | +|antaresRead |2.0.2 | | | | +|apa |0.2.0 | | | | +|ApacheLogProcessor |0.2.2 | | | | +|APSIM |0.9.2 | | | | +|[aqp](problems.md#aqp) |1.15 |1 | | | +|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__ |1 | +|[banxicoR](problems.md#banxicor) |0.9.0 | | |1 | +|[basecallQC](problems.md#basecallqc) |1.0.1 | |1 | | +|[BatchGetSymbols](problems.md#batchgetsymbols) |2.0 | |1 | | +|BAwiR |1.0 | | | | +|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](problems.md#bib2df) |1.0.0 |1 | | | +|bibliometrix |1.9 | | | | +|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 |0.3.3 |-1 | | | +|biomartr |0.7.0 | | | | +|[blastula](problems.md#blastula) |0.1 | | |1 | +|[blkbox](problems.md#blkbox) |1.0 | | |2 | +|blogdown |0.5 | | | | +|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 |0.0.4 | | | | +|[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 |1.2.0 | | | | +|ck37r |1.0.0 | | | | +|ClimClass |2.1.0 | | | | +|[CLME](problems.md#clme) |2.0-8 | |1 | | +|CoFRA |? | | | | +|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 | +|[crossword.r](problems.md#crosswordr) |0.3.5 | | |1 | +|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 | |3 | +|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 |0.7.4 | | | | +|[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) |1.3.0 | |1 | | +|descriptr |0.3.0 | | | | +|detector |0.1.0 | | | | +|devFunc |0.1 | | | | +|[DEXSeq](problems.md#dexseq) |1.22.0 | |1 |1 | +|DiagrammeR |0.9.2 | | | | +|diceR |0.3.2 | | | | +|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 |5.0.0 | | | | +|[driftR](problems.md#driftr) |1.0.0 | | |1 | +|drLumi |0.1.2 | | | | +|[dtree](problems.md#dtree) |0.4.2 | |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 |1.1.1 | | | | +|[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 | |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 | |2 |2 | +|[EventStudy](problems.md#eventstudy) |0.34 | | |2 | +|Evomorph |0.9 | | | | +|exampletestr |1.2.0 | | | | +|[exsic](problems.md#exsic) |1.1.1 | | |1 | +|eyelinker |0.1 | | | | +|ez |4.4-0 | | | | +|[fastLink](problems.md#fastlink) |0.3.0 |1 | | | +|fbar |0.3.4 | | | | +|[fbRanks](problems.md#fbranks) |2.0 | | |2 | +|[FedData](problems.md#feddata) |2.5.1 | |1 | | +|[fergm](problems.md#fergm) |0.2.1 | |1 | | +|[FFTrees](problems.md#fftrees) |1.3.5 | | |1 | +|Fgmutils |0.9.4 | | | | +|[filesstrings](problems.md#filesstrings) |2.0.2 | | |1 | +|[fitbitScraper](problems.md#fitbitscraper) |0.1.8 | |1 | | +|[fivethirtyeight](problems.md#fivethirtyeight) |0.3.0 | | |3 | +|flextable |0.4.2 | | | | +|[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) |0.2.0 | |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 |1.0.1 | | | | +|[genderizeR](problems.md#genderizer) |2.0.0 | | |1 | +|genemodel |1.1.0 | | | | +|geniusr |1.0.0 | | | | +|[GenomicInteractions](problems.md#genomicinteractions) |1.10.0 | |1 |1 | +|[GenomicTools](problems.md#genomictools) |0.2.6 | |1 | | +|geoparser |0.1.1 | | | | +|[geotopbricks](problems.md#geotopbricks) |1.4 | |1 | | +|GERGM |0.11.2 | | | | +|GetDFPData |0.5 | | | | +|GetHFData |1.5 | | | | +|GetITRData |0.6 | | | | +|GetLattesData |0.9 | | | | +|GetTDData |1.3 | | | | +|[gfcanalysis](problems.md#gfcanalysis) |1.4 | |1 | | +|[ggenealogy](problems.md#ggenealogy) |0.3.0 | | |2 | +|[ggformula](problems.md#ggformula) |0.6.1 | |1 |1 | +|ggmap |2.6.1 | | | | +|[ggplotAssist](problems.md#ggplotassist) |0.1.3 | | |1 | +|ggplotgui |1.0.0 | | | | +|[ggraptR](problems.md#ggraptr) |1.0 | |1 |1 | +|gitlabr |0.9 | | | | +|glue |1.2.0 | | | | +|[GOexpress](problems.md#goexpress) |1.10.0 | | |2 | +|[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) |0.1.4 | | |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) |1.11.2 | | |1 | +|[HTSSIP](problems.md#htssip) |1.3.2 |1 |1 |2 | +|HURDAT |0.1.0 | | | | +|[hurricaneexposure](problems.md#hurricaneexposure) |0.0.1 | | |1 | +|[huxtable](problems.md#huxtable) |2.0.0 |1 | |1 | +|hybridModels |0.2.15 | | | | +|[HydeNet](problems.md#hydenet) |0.10.7 |2 |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](problems.md#imager) |0.40.2 |1 | |1 | +|infer |0.1.1 | | | | +|inferr |0.2.0 | | | | +|[io](problems.md#io) |0.3.0 | |1 | | +|[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 | +|jcext |0.1 | | | | +|[jpmesh](problems.md#jpmesh) |1.0.1 | | |2 -1 | +|[JunctionSeq](problems.md#junctionseq) |1.6.0 | |1 |3 | +|[kableExtra](problems.md#kableextra) |0.7.0 | |1 |1 | +|kehra |0.1 | | | | +|keyringr |0.4.0 | | | | +|kgschart |1.3.5 | | | | +|knitr |1.19 | | | | +|kntnr |0.4.1 | | | | +|[kokudosuuchi](problems.md#kokudosuuchi) |0.4.2 | | |1 | +|[KoNLP](problems.md#konlp) |0.80.1 | | |1 | +|[kstIO](problems.md#kstio) |0.1-0 | |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) |1.4.0 | | |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 | |2 |1 | +|matlabr |1.4.3 | | | | +|mau |0.1.2 | | | | +|[MazamaSpatialUtils](problems.md#mazamaspatialutils) |0.5.2 | |1 | | +|MazamaWebUtils |0.1.5 | | | | +|mem |2.11 | | | | +|[memapp](problems.md#memapp) |2.7 | | |1 | +|[metacoder](problems.md#metacoder) |0.2.0 | |1 |1 | +|[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 |1 | +|[mmnet](problems.md#mmnet) |1.13.0 |1 | | | +|moderndive |0.1.1 | | | | +|[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 |-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](problems.md#nandb) |0.2.1 |1 | | | +|narray |0.4.0 | | | | +|[nauf](problems.md#nauf) |1.1.0 | |1 | | +|net.security |0.3.0 | | | | +|[netgen](problems.md#netgen) |1.3 | |1 | | +|networkreporting |0.1.1 | | | | +|neuroim |0.0.6 | | | | +|[NFP](problems.md#nfp) |0.99.2 | | |2 | +|ngstk |0.2.1 | | | | +|nhanesA |0.6.4.3.3 | | | | 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| |1 | diff --git a/revdep/email.yml b/revdep/email.yml index 92dac88a..6dc102ff 100644 --- a/revdep/email.yml +++ b/revdep/email.yml @@ -1,5 +1,5 @@ -release_date: Jan 26 -rel_release_date: one month +release_date: Jan 29 +rel_release_date: day release_version: 1.3.0 my_news_url: https://github.com/tidyverse/stringr/blob/master/NEWS.md diff --git a/revdep/problems.md b/revdep/problems.md index 49222bf4..123be7f6 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,41 +1,19 @@ # abjutils -Version: 0.0.1 +Version: 0.2.1 ## In both -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - ── 4. Failure: rm_accent is the converted version of a string with all non-ASCII - rm_accent(umlaut) not equal to `nudeUmlaut`. - 1/1 mismatches - x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y" - y[1]: "aeiouAEIOUy" - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 10 SKIPPED: 0 FAILED: 4 - 1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) - 2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) - 3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) - 4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) - - Error: testthat unit tests failed - Execution halted - ``` - * checking dependencies in R code ... NOTE ``` Namespaces in Imports field not imported from: - ‘devtools’ ‘httr’ + ‘httr’ ‘progress’ All declared Imports should be used. ``` # afex -Version: 0.18-0 +Version: 0.19-1 ## In both @@ -43,6 +21,7 @@ Version: 0.18-0 ``` Found the following significant warnings: Warning: package ‘lme4’ was built under R version 3.4.3 + Warning: package ‘emmeans’ 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. ``` @@ -61,6 +40,7 @@ Version: 1.2.2 ``` Found the following significant warnings: Warning: package ‘pracma’ was built under R version 3.4.3 + Warning: package ‘sp’ was built under R version 3.4.3 Warning: package ‘rgl’ was built under R version 3.4.3 Warning: package ‘reshape2’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/AFM/new/AFM.Rcheck/00install.out’ for details. @@ -127,6 +107,15 @@ Version: 1.2.0 * checking examples ... ERROR ``` ... + The following object is masked from ‘package:DelayedArray’: + + type + + The following object is masked from ‘package:base’: + + strsplit + + Loading required package: Rsamtools > library(rtracklayer) > gap <- ERR188088() snapshotDate(): 2016-10-01 @@ -135,18 +124,9 @@ Version: 1.2.0 > 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 -> + Error in value[[3L]](cond) : 'asBam' truncated input file at record 29582 + SAM file: '/Users/hadley/Documents/tidyverse/stringr/revdep/library.noindex/alpine/alpineData/extdata/ERR188088.sam' + Calls: export ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted ``` @@ -184,6 +164,66 @@ Version: 1.0 Compose cutPoints ``` +# annovarR + +Version: 1.0.0 + +## In both + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + vcfanno_linux64 -p 2 /Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/annovarR/new/annovarR.Rcheck/annovarR/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf + ── 1. Error: select.dat.full.match (@test_utils.R#22) ───────────────────────── + Failed to connect to database: Access denied for user ''@'localhost' to database 'annovarr' + 1: dbConnect(RMySQL::MySQL(), dbname = "annovarr") at testthat/test_utils.R:22 + 2: dbConnect(RMySQL::MySQL(), dbname = "annovarr") + 3: .local(drv, ...) + + INFO [2018-01-29 07:45:03] info.msg + [1] "print.vb" + ══ testthat results ═══════════════════════════════════════════════════════════ + OK: 90 SKIPPED: 0 FAILED: 1 + 1. Error: select.dat.full.match (@test_utils.R#22) + + Error: testthat unit tests failed + Execution halted + ``` + +# aqp + +Version: 1.15 + +## In both + +* checking examples ... ERROR + ``` + ... + + data(loafercreek) + + + + # extract first 15 profiles + + x <- loafercreek[1:15, ] + + s <- site(x) + + + + # plot + + par(mar=c(0,0,0,0)) + + plot(x, name='hzname', id.style='top') + + + + # add brackets describing the argillic horizon + + addDiagnosticBracket(x, 'argillic horizon', col='red') + + # add brackets describing paralithic contact + + addDiagnosticBracket(x, 'paralithic contact', col='blue') + + } + Loading required package: soilDB + Warning: package ‘soilDB’ was built under R version 3.4.3 + Error in segments(x.1, top[plot.order], x.2, top[plot.order], lend = 2, : + cannot mix zero-length and non-zero-length coordinates + Calls: addDiagnosticBracket -> addBracket -> segments + Execution halted + ``` + # asciiSetupReader Version: 1.2 @@ -202,8 +242,22 @@ Version: 1.0.5 ## In both -* R CMD check timed out - +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Warning: package 'VennDiagram' was built under R version 3.4.3 + See system.file("LICENSE", package="MotifDb") for use restrictions. + The signal is being calculated for DNA-seq. + The signal is being calculated for DNA-seq. + Warning in .Call2("XString_match_PWM", pwm, subject, min.score, count.only, : + 'subject' contains letters not in [ACGT] ==> assigned weight 0 to them + Warning in .Call2("XString_match_PWM", pwm, subject, min.score, count.only, : + 'subject' contains letters not in [ACGT] ==> assigned weight 0 to them + Error: processing vignette 'ATACseqQC.Rmd' failed with diagnostics: + path for html_dependency not found: + Execution halted + ``` * checking installed package size ... NOTE ``` @@ -234,6 +288,7 @@ Version: 1.0.0 ``` Found the following significant warnings: Warning: package ‘rstan’ was built under R version 3.4.3 + Warning: package ‘StanHeaders’ 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. ``` @@ -260,6 +315,18 @@ Version: 1.0.0 Version: 0.2.0 +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Quitting from lines 86-96 (geocode.Rmd) + Error: processing vignette 'geocode.Rmd' failed with diagnostics: + The API sent back an error 502 + Execution halted + ``` + ## In both * checking dependencies in R code ... NOTE @@ -288,11 +355,23 @@ 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. ``` +# BatchGetSymbols + +Version: 2.0 + +## In both + +* checking whether package ‘BatchGetSymbols’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘xml2’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/BatchGetSymbols/new/BatchGetSymbols.Rcheck/00install.out’ for details. + ``` + # bea.R Version: 1.0.4 @@ -335,6 +414,33 @@ Version: 2.2.1 Checking should be performed on sources prepared by ‘R CMD build’. ``` +# bib2df + +Version: 1.0.0 + +## In both + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + > library("testthat") + Warning message: + package 'testthat' was built under R version 3.4.3 + > library("bib2df") + > test_check("bib2df") + ── 1. Failure: bib2df() throws error messages (@tests.R#53) ─────────────────── + `bib2df("https://www.ottlngr.de/data/x.bib")` did not throw an error. + + ══ testthat results ═══════════════════════════════════════════════════════════ + OK: 15 SKIPPED: 0 FAILED: 1 + 1. Failure: bib2df() throws error messages (@tests.R#53) + + Error: testthat unit tests failed + Execution halted + ``` + # BiGGR Version: 1.12.0 @@ -407,7 +513,6 @@ 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. ``` @@ -480,74 +585,6 @@ Version: 1.2.0 See the note in ?`:::` about the use of this operator. ``` -# BioInstaller - -Version: 0.3.1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - } - typeName = gsub("^CURLE_", "", typeName) - fun = (if (asError) - stop - else warning) - fun(structure(list(message = msg, call = sys.call()), class = c(typeName, "GenericCurlError", - "error", "condition"))) - }(28L, "", TRUE) - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 69 SKIPPED: 0 FAILED: 1 - 1. Error: download.file.custom is.dir (@test_utils.R#138) - - Error: testthat unit tests failed - Execution halted - ``` - -# biomartr - -Version: 0.5.2 - -## Newly fixed - -* checking tests ... - ``` - ERROR - 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 2243299 bytes (2.1 MB) - ================================================== - trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt' - 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 666851 bytes (651 KB) - ================================================== - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 5 SKIPPED: 60 FAILED: 1 - 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 97-112 (Functional_Annotation.Rmd) - Error: processing vignette 'Functional_Annotation.Rmd' failed with diagnostics: - The given dataset: hsapiens_gene_ensembl , is not valid. Correct dataset names can be obtained with the listDatasets() function. - Execution halted - ``` - # blastula Version: 0.1 @@ -689,7 +726,6 @@ 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 @@ -850,9 +886,9 @@ Version: 1.4.0 * checking installed package size ... NOTE ``` - installed size is 18.7Mb + installed size is 18.5Mb sub-directories of 1Mb or more: - data 18.0Mb + data 17.8Mb ``` * checking R code for possible problems ... NOTE @@ -1027,6 +1063,19 @@ Version: 1.2.0 Packages unavailable to check Rd xrefs: ‘PADOG’, ‘GeneMeta’ ``` +# crossword.r + +Version: 0.3.5 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘dplyr’ ‘r6extended’ + All declared Imports should be used. + ``` + # ctsGE Version: 1.2.0 @@ -1193,31 +1242,8 @@ Version: 1.16.0 ## In both -* checking examples ... ERROR - ``` - ... - > ### Title: prepare annotation for Refseq - > ### Aliases: PrepareAnnotationRefseq - > - > ### ** Examples - > - > - > transcript_ids <- c("NM_001126112", "NM_033360", "NR_073499", "NM_004448", - + "NM_000179", "NR_029605", "NM_004333", "NM_001127511") - > pepfasta <- system.file("extdata", "refseq_pro_seq.fasta", - + package="customProDB") - > CDSfasta <- system.file("extdata", "refseq_coding_seq.fasta", - + package="customProDB") - > annotation_path <- tempdir() - > PrepareAnnotationRefseq(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: PrepareAnnotationRefseq ... trackNames -> .local -> ucscTracks -> ucscTracks -> .local - Execution halted - ``` +* R CMD check timed out + * checking DESCRIPTION meta-information ... NOTE ``` @@ -1259,32 +1285,6 @@ Version: 1.16.0 protAcc rsid saveDb transcript txname ``` -* checking re-building of vignette outputs ... NOTE - ``` - ... - lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, - pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, - setdiff, sort, table, tapply, union, unique, unsplit, which, - which.max, which.min - - Loading required package: S4Vectors - - Attaching package: ‘S4Vectors’ - - The following object is masked from ‘package:base’: - - expand.grid - - Loading required package: IRanges - Loading required package: GenomeInfoDb - - Error: processing vignette 'customProDB.Rnw' failed with diagnostics: - chunk 1 (label = dbSNPversion) - Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) : - 'names' attribute [212] must be the same length as the vector [210] - Execution halted - ``` - # d3Tree Version: 0.2.0 @@ -1317,49 +1317,6 @@ Version: 1.0 All declared Imports should be used. ``` -# data.tree - -Version: 0.7.3 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 10 ¦--Go agile 250000 - 11 °--Switch to R 50000 - levelName b 1 - 1 Root NA - 2 °--a 2 - 3 °--c NA 1, 2, 3, 4, 5 - levelName a - 1 Root - 2 °--a 2 - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 352 SKIPPED: 2 FAILED: 1 - 1. Error: partykid (@test-treeConversionParty.R#37) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in engine$weave(file, quiet = quiet, encoding = enc) : - The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. - Warning: package 'yaml' was built under R version 3.4.3 - Warning in engine$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 512-515 (data.tree.Rmd) - Error: processing vignette 'data.tree.Rmd' failed with diagnostics: - there is no package called 'webshot' - Execution halted - ``` - # datacheck Version: 1.2.2 @@ -1444,16 +1401,9 @@ 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 +Version: 1.3.0 ## In both @@ -1464,28 +1414,19 @@ Version: 1.2.5 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/DeLorean/new/DeLorean.Rcheck/00install.out’ for details. ``` -* checking S3 generic/method consistency ... WARNING - ``` - filter: - function(x, filter, method, sides, circular, init) - filter.cells: - function(dl, .filter, number, cells) - - filter: - function(x, filter, method, sides, circular, init) - filter.genes: - function(dl, .filter, number, genes) - - See section ‘Generic functions and methods’ in the ‘Writing R - Extensions’ manual. - ``` - # DEXSeq Version: 1.22.0 ## In both +* checking whether package ‘DEXSeq’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘matrixStats’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/DEXSeq/new/DEXSeq.Rcheck/00install.out’ for details. + ``` + * checking package dependencies ... NOTE ``` Depends: includes the non-default packages: @@ -1534,14 +1475,17 @@ Version: 1.0.0 # dtree -Version: 0.2.3 +Version: 0.4.2 ## In both * checking whether package ‘dtree’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘rpart’ was built under R version 3.4.3 Warning: package ‘party’ was built under R version 3.4.3 + Warning: package ‘mvtnorm’ was built under R version 3.4.3 + Warning: package ‘zoo’ was built under R version 3.4.3 Warning: package ‘evtree’ was built under R version 3.4.3 Warning: package ‘partykit’ was built under R version 3.4.3 Warning: package ‘libcoin’ was built under R version 3.4.3 @@ -1649,25 +1593,6 @@ Version: 0.1.0 All declared Imports should be used. ``` -# eeptools - -Version: 1.1.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - 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: - Package `maps` required for `map_data`. - Please install and try again. - Execution halted - ``` - # eiCompare Version: 2.1 @@ -1679,6 +1604,7 @@ Version: 2.1 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 ‘mvtnorm’ 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. ``` @@ -1689,27 +1615,12 @@ Version: 1.3.3 ## In both -* checking examples ... ERROR +* checking package dependencies ... ERROR ``` - Running examples in ‘elementR-Ex.R’ failed - The error most likely occurred in: + Package required but not available: ‘climtrends’ - > ### Name: elementR_project - > ### Title: Object elementR_project - > ### Aliases: elementR_project - > - > ### ** Examples - > - > ## create a new elementR_repStandard object based on the "filePath" - > ## from a folder containing sample replicate - > - > filePath <- system.file("Example_Session", package="elementR") - > - > exampleProject <- elementR_project$new(filePath) - Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : - [tcl] invalid command name "toplevel". - Calls: ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure - Execution halted + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. ``` # ENCODExplorer @@ -1718,11 +1629,18 @@ Version: 2.2.1 ## In both +* checking whether package ‘ENCODExplorer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘DT’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/ENCODExplorer/new/ENCODExplorer.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` - installed size is 73.8Mb + installed size is 73.6Mb sub-directories of 1Mb or more: - data 24.1Mb + data 23.9Mb doc 1.5Mb extdata 48.0Mb ``` @@ -1845,7 +1763,14 @@ Version: 1.0.0 ## In both -* checking re-building of vignette outputs ... WARNING +* checking whether package ‘EventPointer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘matrixStats’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/EventPointer/new/EventPointer.Rcheck/00install.out’ for details. + ``` + +* checking re-building of vignette outputs ... WARNING ``` ... The following object is masked from 'package:Biostrings': @@ -1865,7 +1790,7 @@ 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/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 + You changed the working directory to /private/tmp/RtmpUOtfKq (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 @@ -1927,7 +1852,7 @@ Version: 1.1.1 # fastLink -Version: 0.2.0 +Version: 0.3.0 ## In both @@ -2005,6 +1930,19 @@ Version: 2.0 contains 'methods'). ``` +# FedData + +Version: 2.5.1 + +## In both + +* checking whether package ‘FedData’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/FedData/new/FedData.Rcheck/00install.out’ for details. + ``` + # fergm Version: 0.2.1 @@ -2015,6 +1953,7 @@ Version: 0.2.1 ``` Found the following significant warnings: Warning: package ‘rstan’ was built under R version 3.4.3 + Warning: package ‘StanHeaders’ 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. ``` @@ -2031,6 +1970,17 @@ Version: 1.3.5 doc 4.6Mb ``` +# filesstrings + +Version: 2.0.2 + +## In both + +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘dplyr’ + ``` + # fitbitScraper Version: 0.1.8 @@ -2058,21 +2008,16 @@ Version: 0.3.0 Package suggested but not available for checking: ‘fivethirtyeight’ ``` -* checking data for non-ASCII characters ... NOTE +* checking installed package size ... NOTE ``` - Note: found 371 marked UTF-8 strings + installed size is 5.2Mb + sub-directories of 1Mb or more: + data 4.4Mb ``` -# flextable - -Version: 0.4.0 - -## In both - -* checking dependencies in R code ... NOTE +* checking data for non-ASCII characters ... NOTE ``` - Namespace in Imports field not imported from: ‘lazyeval’ - All declared Imports should be used. + Note: found 371 marked UTF-8 strings ``` # flowWorkspace @@ -2232,7 +2177,7 @@ Version: 0.1.0 # frequencyConnectedness -Version: 0.1.6 +Version: 0.2.0 ## In both @@ -2240,6 +2185,8 @@ Version: 0.1.6 ``` Found the following significant warnings: Warning: package ‘MASS’ was built under R version 3.4.3 + Warning: package ‘zoo’ was built under R version 3.4.3 + Warning: package ‘pbapply’ 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. ``` @@ -2292,6 +2239,7 @@ Version: 2.1-1 * checking whether package ‘GADMTools’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 Warning: package ‘rgdal’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/GADMTools/new/GADMTools.Rcheck/00install.out’ for details. ``` @@ -2362,9 +2310,9 @@ Version: 0.4.01 * checking installed package size ... NOTE ``` - installed size is 6.9Mb + installed size is 7.0Mb sub-directories of 1Mb or more: - libs 6.5Mb + libs 6.6Mb ``` # genderizeR @@ -2384,6 +2332,13 @@ Version: 1.10.0 ## In both +* checking whether package ‘GenomicInteractions’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘matrixStats’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/GenomicInteractions/new/GenomicInteractions.Rcheck/00install.out’ for details. + ``` + * checking installed package size ... NOTE ``` installed size is 10.9Mb @@ -2405,22 +2360,31 @@ Version: 0.2.6 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/GenomicTools/new/GenomicTools.Rcheck/00install.out’ for details. ``` -# GetITRData +# geotopbricks -Version: 0.6 +Version: 1.4 -## Newly broken +## In both -* checking re-building of vignette outputs ... WARNING +* checking whether package ‘geotopbricks’ can be installed ... 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 + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + Warning: package ‘zoo’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/geotopbricks/new/geotopbricks.Rcheck/00install.out’ for details. + ``` + +# gfcanalysis + +Version: 1.4 + +## In both + +* checking whether package ‘gfcanalysis’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/gfcanalysis/new/gfcanalysis.Rcheck/00install.out’ for details. ``` # ggenealogy @@ -2442,7 +2406,7 @@ Version: 0.3.0 # ggformula -Version: 0.6 +Version: 0.6.1 ## In both @@ -2450,28 +2414,15 @@ Version: 0.6 ``` Error in re-building vignettes: ... - Quitting from lines 187-193 (ggformula.Rmd) + Quitting from lines 345-357 (ggformula.Rmd) Error: processing vignette 'ggformula.Rmd' failed with diagnostics: - there is no package called 'statisticalModeling' + object 'NewYork2013' not found Execution halted ``` * checking package dependencies ... NOTE ``` - Package suggested but not available for checking: ‘statisticalModeling’ - ``` - -# ggmap - -Version: 2.6.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.0Mb - sub-directories of 1Mb or more: - data 4.8Mb + Package suggested but not available for checking: ‘weatherData’ ``` # ggplotAssist @@ -2493,6 +2444,13 @@ Version: 1.0 ## In both +* checking whether package ‘ggraptR’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘shinyjs’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/ggraptR/new/ggraptR.Rcheck/00install.out’ for details. + ``` + * checking dependencies in R code ... NOTE ``` Namespaces in Imports field not imported from: @@ -2508,15 +2466,6 @@ Version: 1.0 Version: 1.10.0 -## Newly fixed - -* checking installed package size ... NOTE - ``` - installed size is 5.0Mb - sub-directories of 1Mb or more: - data 4.3Mb - ``` - ## In both * checking R code for possible problems ... NOTE @@ -2609,7 +2558,7 @@ Version: 0.1 # gutenbergr -Version: 0.1.3 +Version: 0.1.4 ## In both @@ -2650,6 +2599,7 @@ Version: 0.7 ``` Found the following significant warnings: Warning: package ‘rgdal’ was built under R version 3.4.3 + Warning: package ‘sp’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/hddtools/new/hddtools.Rcheck/00install.out’ for details. ``` @@ -2685,7 +2635,7 @@ Version: 0.3.2 # htmlTable -Version: 1.11.1 +Version: 1.11.2 ## In both @@ -2696,7 +2646,7 @@ Version: 1.11.1 # HTSSIP -Version: 1.3.0 +Version: 1.3.2 ## In both @@ -2706,7 +2656,7 @@ Version: 1.3.0 Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 57 SKIPPED: 23 FAILED: 11 + OK: 83 SKIPPED: 17 FAILED: 11 1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9) 3. Error: phyloseq sim (@test-HTSSIP_sim.R#59) @@ -2714,7 +2664,7 @@ Version: 1.3.0 5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) - 8. Error: phyloseq-rep sample_data can be converted to dataframe (@test-Util.R#35) + 8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#35) 9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 1. ... @@ -2750,7 +2700,7 @@ Version: 1.3.0 * checking installed package size ... NOTE ``` - installed size is 5.3Mb + installed size is 5.5Mb sub-directories of 1Mb or more: data 4.4Mb ``` @@ -2772,19 +2722,44 @@ Version: 0.0.1 Package suggested but not available for checking: ‘hurricaneexposuredata’ ``` -# HydeNet +# huxtable -Version: 0.10.6 +Version: 2.0.0 -## Newly broken +## In both -* checking whether package ‘HydeNet’ can be installed ... ERROR +* checking tests ... ``` - Installation failed. - See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/HydeNet/new/HydeNet.Rcheck/00install.out’ for details. + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message) + 7: withVisible(code) + 8: eval_bare(get_expr(quo), get_env(quo)) + 9: rmarkdown::render("table-tester-2.Rmd", quiet = TRUE, output_format = "pdf_document") + 10: convert(output_file, run_citeproc) at /private/tmp/RtmpSJUE4K/R.INSTALLa89f74d1cb69/rmarkdown/R/render.R:661 + 11: pandoc_convert(utf8_input, pandoc_to, output_format$pandoc$from, output, citeproc, + output_format$pandoc$args, !quiet) at /private/tmp/RtmpSJUE4K/R.INSTALLa89f74d1cb69/rmarkdown/R/render.R:593 + 12: stop("pandoc document conversion failed with error ", result, call. = FALSE) at /private/tmp/RtmpSJUE4K/R.INSTALLa89f74d1cb69/rmarkdown/R/pandoc.R:100 + + ══ testthat results ═══════════════════════════════════════════════════════════ + OK: 301 SKIPPED: 48 FAILED: 1 + 1. Error: table-tester-2.Rmd renders without errors in LaTeX (@test-with-pandoc.R#27) + + Error: testthat unit tests failed + Execution halted ``` -## Newly fixed +* checking Rd cross-references ... NOTE + ``` + Package unavailable to check Rd xrefs: ‘xtable’ + ``` + +# HydeNet + +Version: 0.10.7 + +## In both * checking examples ... ERROR ``` @@ -2852,45 +2827,6 @@ Version: 0.10.6 Execution halted ``` -## Installation - -### Devel - -``` -* installing *source* package ‘HydeNet’ ... -** package ‘HydeNet’ successfully unpacked and MD5 sums checked -** R -** data -*** moving datasets to lazyload DB -Warning: namespace ‘HydeNet’ is not available and has been replaced -by .GlobalEnv when processing object ‘BlackJack’ -Warning: namespace ‘HydeNet’ is not available and has been replaced -by .GlobalEnv when processing object ‘BlackJack’ -** inst -** preparing package for lazy loading -Error : object ‘perl’ is not exported by 'namespace:stringr' -ERROR: lazy loading failed for package ‘HydeNet’ -* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/HydeNet/new/HydeNet.Rcheck/HydeNet’ - -``` -### CRAN - -``` -* installing *source* package ‘HydeNet’ ... -** package ‘HydeNet’ successfully unpacked and MD5 sums checked -** R -** data -*** moving datasets to lazyload DB -** inst -** preparing package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded -* DONE (HydeNet) - -``` # hydroscoper Version: 0.1.0 @@ -2978,7 +2914,7 @@ Version: 2.3.1 * checking installed package size ... NOTE ``` - installed size is 8.1Mb + installed size is 8.0Mb sub-directories of 1Mb or more: R 2.4Mb data 2.0Mb @@ -3013,6 +2949,102 @@ 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’ + +``` +# io + +Version: 0.3.0 + +## In both + +* checking whether package ‘io’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘filenamer’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/io/new/io.Rcheck/00install.out’ for details. + ``` + # IONiseR Version: 2.0.0 @@ -3079,10 +3111,30 @@ 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 +## Newly fixed + +* checking installed package size ... NOTE + ``` + installed size is 5.3Mb + sub-directories of 1Mb or more: + R 4.4Mb + ``` + ## In both * checking dependencies in R code ... NOTE @@ -3102,6 +3154,13 @@ Version: 1.6.0 ## In both +* checking whether package ‘JunctionSeq’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘matrixStats’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/JunctionSeq/new/JunctionSeq.Rcheck/00install.out’ for details. + ``` + * checking package dependencies ... NOTE ``` Packages which this enhances but not available for checking: ‘Cairo’ ‘pryr’ @@ -3130,7 +3189,7 @@ Version: 1.6.0 # kableExtra -Version: 0.6.1 +Version: 0.7.0 ## In both @@ -3153,36 +3212,26 @@ Version: 0.6.1 ! Missing number, treated as zero. { - l.612 \linewidth { + l.614 \linewidth { Error: processing vignette 'awesome_table_in_pdf.Rmd' failed with diagnostics: pandoc document conversion failed with error 43 Execution halted ``` -# knitr - -Version: 1.18 - -## Newly broken - -* checking dependencies in R code ... NOTE +* checking installed package size ... NOTE ``` - Missing or unexported object: ‘stringr::perl’ + installed size is 5.5Mb + sub-directories of 1Mb or more: + doc 5.3Mb ``` # kokudosuuchi -Version: 0.4.1 +Version: 0.4.2 ## In both -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘stringi’ - All declared Imports should be used. - ``` - * checking data for non-ASCII characters ... NOTE ``` Note: found 52458 marked UTF-8 strings @@ -3201,6 +3250,20 @@ Version: 0.80.1 java 6.0Mb ``` +# kstIO + +Version: 0.1-0 + +## In both + +* checking whether package ‘kstIO’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sets’ 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/kstIO/new/kstIO.Rcheck/00install.out’ for details. + ``` + # leaflet.esri Version: 0.2 @@ -3228,7 +3291,7 @@ Version: 0.2 # lidR -Version: 1.3.1 +Version: 1.4.0 ## In both @@ -3370,6 +3433,7 @@ Version: 1.7 ``` Found the following significant warnings: Warning: package ‘rgl’ was built under R version 3.4.3 + Warning: package ‘magic’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/Maeswrap/new/Maeswrap.Rcheck/00install.out’ for details. ``` @@ -3439,14 +3503,21 @@ Version: 1.2.1 ## In both +* checking whether package ‘MAST’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘matrixStats’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/MAST/new/MAST.Rcheck/00install.out’ for details. + ``` + * checking re-building of vignette outputs ... WARNING ``` 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 + Warning: package 'matrixStats' was built under R version 3.4.3 Quitting from lines 90-102 (MAITAnalysis.Rmd) Error: processing vignette 'MAITAnalysis.Rmd' failed with diagnostics: Columns in 'columns' not found in data: c('PC1', 'PC2', 'PC3'). Choices: c('V1', 'V2', 'V3', 'V4', 'wellKey', 'condition', 'nGeneOn', 'libSize', 'PercentToHuman', 'MedianCVCoverage', 'PCRDuplicate', 'exonRate', 'pastFastqc', 'ncells', 'ngeneson', 'cngeneson', 'TRAV1', 'TRBV6', 'TRBV4', 'TRBV20', 'alpha', 'beta', 'ac', 'bc', 'ourfilter') @@ -3461,18 +3532,51 @@ Version: 1.2.1 doc 1.9Mb ``` +# MazamaSpatialUtils + +Version: 0.5.2 + +## In both + +* checking whether package ‘MazamaSpatialUtils’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/MazamaSpatialUtils/new/MazamaSpatialUtils.Rcheck/00install.out’ for details. + ``` + # memapp -Version: 2.6 +Version: 2.7 ## In both * checking dependencies in R code ... NOTE ``` Namespaces in Imports field not imported from: - ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘formattable’ ‘ggplot2’ ‘ggthemes’ ‘mem’ - ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’ - ‘shinythemes’ ‘stringr’ + ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘formattable’ ‘ggplot2’ + ‘ggthemes’ ‘magrittr’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ + ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’ + All declared Imports should be used. + ``` + +# metacoder + +Version: 0.2.0 + +## In both + +* checking whether package ‘metacoder’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘taxa’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/metacoder/new/metacoder.Rcheck/00install.out’ for details. + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ggrepel’ ‘reshape’ All declared Imports should be used. ``` @@ -3782,7 +3886,21 @@ Version: 0.0.1 ## In both -* checking dependencies in R code ... NOTE +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Warning in isNamespace(frame) : + closing unused connection 6 (http://gd2.mlb.com/components/game/mlb//year_2016/month_04/day_21/gid_2016_04_21_seamlb_clemlb_1/inning/inning_all.xml) + Warning in isNamespace(frame) : + closing unused connection 5 (http://gd2.mlb.com/components/game/mlb//year_2016/month_04/day_21/gid_2016_04_21_lanmlb_atlmlb_1/inning/inning_all.xml) + Quitting from lines 22-32 (pitch_plotting.Rmd) + Error: processing vignette 'pitch_plotting.Rmd' failed with diagnostics: + `by` can't contain join column `batter` which is missing from LHS + Execution halted + ``` + +* checking dependencies in R code ... NOTE ``` Namespaces in Imports field not imported from: ‘doParallel’ ‘iterators’ ‘parallel’ @@ -3850,30 +3968,14 @@ Version: 2.4.0 ## Newly fixed -* checking re-building of vignette outputs ... WARNING +* R CMD check timed out + + +* checking whether package ‘monocle’ can be installed ... WARNING ``` - ... - the condition has length > 1 and only the first element will be used - Warning in if (method == "num_genes") { : - the condition has length > 1 and only the first element will be used - Warning in if (method == "num_genes") { : - the condition has length > 1 and only the first element will be used - Warning in if (method == "num_genes") { : - the condition has length > 1 and only the first element will be used - Warning in if (method == "num_genes") { : - the condition has length > 1 and only the first element will be used - Warning in if (method == "num_genes") { : - the condition has length > 1 and only the first element will be used - Warning: Deprecated, use tibble::rownames_to_column() instead. - Warning: Removed 3576038 rows containing non-finite values (stat_density). - Warning: Deprecated, use tibble::rownames_to_column() instead. - Warning: Deprecated, use tibble::rownames_to_column() instead. - Warning: Transformation introduced infinite values in continuous y-axis - Warning: Transformation introduced infinite values in continuous y-axis - Quitting from lines 327-334 (monocle-vignette.Rnw) - Error: processing vignette 'monocle-vignette.Rnw' failed with diagnostics: - BLAS/LAPACK routine 'DLASCL' gave error code -4 - Execution halted + Found the following significant warnings: + Warning: package ‘irlba’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/monocle/old/monocle.Rcheck/00install.out’ for details. ``` * checking R code for possible problems ... NOTE @@ -3910,6 +4012,7 @@ Version: 2.4.0 *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading +Warning: package ‘irlba’ was built under R version 3.4.3 Error : object ‘str_join’ is not exported by 'namespace:stringr' ERROR: lazy loading failed for package ‘monocle’ * removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/monocle/new/monocle.Rcheck/monocle’ @@ -3924,11 +4027,13 @@ ERROR: lazy loading failed for package ‘monocle’ *** moving datasets to lazyload DB ** inst ** preparing package for lazy loading +Warning: package ‘irlba’ was built under R version 3.4.3 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded +Warning: package ‘irlba’ was built under R version 3.4.3 * DONE (monocle) ``` @@ -4102,6 +4207,7 @@ Version: 1.0 * checking whether package ‘mtk’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘lhs’ was built under R version 3.4.3 Warning: package ‘rgl’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/mtk/new/mtk.Rcheck/00install.out’ for details. ``` @@ -4183,6 +4289,20 @@ Version: 1.10.0 to your NAMESPACE file. ``` +# nandb + +Version: 0.2.1 + +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘autothresholdr’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + # nauf Version: 1.1.0 @@ -4198,6 +4318,20 @@ Version: 1.1.0 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/nauf/new/nauf.Rcheck/00install.out’ for details. ``` +# netgen + +Version: 1.3 + +## In both + +* checking whether package ‘netgen’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘mvtnorm’ was built under R version 3.4.3 + Warning: package ‘lhs’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/netgen/new/netgen.Rcheck/00install.out’ for details. + ``` + # NFP Version: 0.99.2 @@ -4222,6 +4356,13 @@ Version: 0.6.5 ## In both +* checking whether package ‘Nippon’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/Nippon/new/Nippon.Rcheck/00install.out’ for details. + ``` + * checking Rd cross-references ... NOTE ``` Packages unavailable to check Rd xrefs: ‘cshapes’, ‘mapdata’, ‘timeDate’, ‘TimeWarp’, ‘Holidays’ @@ -4271,7 +4412,7 @@ Version: 0.20.6 # NNS -Version: 0.3.8.1 +Version: 0.3.8.2 ## In both @@ -4301,6 +4442,19 @@ Version: 0.1.0 All declared Imports should be used. ``` +# optim.functions + +Version: 0.1 + +## In both + +* checking whether package ‘optim.functions’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘lhs’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/optim.functions/new/optim.functions.Rcheck/00install.out’ for details. + ``` + # P2C2M Version: 0.7.6 @@ -4386,6 +4540,19 @@ Version: 1.1.0 Malformed Title field: should not end in a period. ``` +# PersomicsArray + +Version: 1.0 + +## In both + +* checking whether package ‘PersomicsArray’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/PersomicsArray/new/PersomicsArray.Rcheck/00install.out’ for details. + ``` + # PGA Version: 1.6.0 @@ -4396,25 +4563,25 @@ Version: 1.6.0 ``` ... - > ### Name: PrepareAnnotationRefseq2 - > ### Title: Prepare annotation from Refseq - > ### Aliases: PrepareAnnotationRefseq2 + > ### Name: PrepareAnnotationEnsembl2 + > ### Title: Prepare annotation from ENSEMBL + > ### Aliases: PrepareAnnotationEnsembl2 > > ### ** Examples > - > 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") + > ensembl <- biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", + + host="grch37.ensembl.org", path="/biomart/martservice", + + archive=FALSE) + > > 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 + > transcript_ids <- c("ENST00000234420", "ENST00000269305", "ENST00000445888") + > + > PrepareAnnotationEnsembl2(mart=ensembl, annotation_path=annotation_path, + + splice_matrix=FALSE, dbsnp=NULL, transcript_ids=transcript_ids, + + COSMIC=FALSE) + Prepare gene/transcript/protein id mapping information (ids.RData) ... Error in getBM(attributes = attributes.id, mart = mart, filters = "ensembl_transcript_id", : + Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_91: DBI connect('database=ensembl_mart_91;host=hh-mysql-ens-grch37mart-web;port=4560','ensro',...) failed: Can't connect to MySQL server on 'hh-mysql-ens-grch37mart-web' (111) at /nfs/public/release/ensweb/latest/live/grch37-mart/www_91/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98. + Calls: PrepareAnnotationEnsembl2 -> getBM Execution halted ``` @@ -4466,6 +4633,49 @@ Version: 1.6.0 transcript tx_name txid txname varbase writeXStringSet x xyz y ``` +# phrasemachine + +Version: 1.1.2 + +## In both + +* checking tests ... + ``` + ERROR + Running the tests in ‘tests/testthat.R’ failed. + Last 13 lines of output: + 4: getNamespace(ns) + 5: tryCatch(loadNamespace(name), error = function(e) stop(e)) + 6: tryCatchList(expr, classes, parentenv, handlers) + 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) + 8: value[[3L]](cond) + + Currently tagging document 1 of 1 + Extracting phrases from document 1 of 1 + ══ testthat results ═══════════════════════════════════════════════════════════ + OK: 10 SKIPPED: 0 FAILED: 2 + 1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#5) + 2. Error: See if extractor works (@test_extract_phrases.R#5) + + Error: testthat unit tests failed + Execution halted + ``` + +* checking re-building of vignette outputs ... WARNING + ``` + Error in re-building vignettes: + ... + Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) + Error: processing vignette 'getting_started_with_phrasemachine.Rmd' failed with diagnostics: + there is no package called 'quanteda' + Execution halted + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘quanteda’ + ``` + # pkgmaker Version: 0.22 @@ -4525,6 +4735,17 @@ Version: 2.1.1 All declared Imports should be used. ``` +# plotKML + +Version: 0.5-8 + +## In both + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘adehabitat’ + ``` + # pointblank Version: 0.1 @@ -4538,6 +4759,20 @@ Version: 0.1 All declared Imports should be used. ``` +# politeness + +Version: 0.2.1 + +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘quanteda’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + # polywog Version: 0.4-0 @@ -4578,6 +4813,19 @@ Version: 0.4-0 to your NAMESPACE file. ``` +# postGIStools + +Version: 0.2.1 + +## In both + +* checking whether package ‘postGIStools’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/postGIStools/new/postGIStools.Rcheck/00install.out’ for details. + ``` + # primerTree Version: 1.0.3 @@ -4659,8 +4907,17 @@ Version: 1.9.1 ## In both -* R CMD check timed out - +* 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 + ``` * checking installed package size ... NOTE ``` @@ -4731,7 +4988,7 @@ Version: 0.2.1 # PWFSLSmoke -Version: 0.99.33 +Version: 1.0.10 ## In both @@ -4739,6 +4996,7 @@ Version: 0.99.33 ``` Found the following significant warnings: Warning: package ‘MazamaSpatialUtils’ was built under R version 3.4.3 + Warning: package ‘sp’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/PWFSLSmoke/new/PWFSLSmoke.Rcheck/00install.out’ for details. ``` @@ -4918,10 +5176,16 @@ Version: 1.8.0 Execution halted ``` +* checking whether package ‘rcellminer’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘fingerprint’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/rcellminer/new/rcellminer.Rcheck/00install.out’ for details. + ``` + * checking re-building of vignette outputs ... WARNING ``` ... - duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, @@ -4937,6 +5201,7 @@ Version: 1.8.0 Loading required package: rcdklibs Loading required package: rJava Loading required package: fingerprint + Warning: package 'fingerprint' was built under R version 3.4.3 Loading required package: rcellminerData Quitting from lines 118-119 (rcellminerUsage.Rmd) Error: processing vignette 'rcellminerUsage.Rmd' failed with diagnostics: @@ -4989,6 +5254,17 @@ Version: 1.8.0 contains 'methods'). ``` +# rclimateca + +Version: 1.0.0 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 24 marked UTF-8 strings + ``` + # rClinicalCodes Version: 1.0.1 @@ -5018,13 +5294,6 @@ 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 @@ -5043,52 +5312,16 @@ Version: 0.1 # redcapAPI -Version: 1.3 +Version: 2.0 ## In both -* checking whether package ‘redcapAPI’ can be installed ... ERROR +* checking dependencies in R code ... NOTE ``` - Installation failed. - See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/redcapAPI/new/redcapAPI.Rcheck/00install.out’ for details. + Namespace in Imports field not imported from: ‘DBI’ + All declared Imports should be used. ``` -## Installation - -### Devel - -``` -* installing *source* package ‘redcapAPI’ ... -** package ‘redcapAPI’ successfully unpacked and MD5 sums checked -** libs -ccache clang -Qunused-arguments -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o -ccache clang -Qunused-arguments -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o redcapAPI.so Rinit.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to /Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/redcapAPI/new/redcapAPI.Rcheck/redcapAPI/libs -** R -** inst -** preparing package for lazy loading -Error : object ‘[.labelled’ is not exported by 'namespace:Hmisc' -ERROR: lazy loading failed for package ‘redcapAPI’ -* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/redcapAPI/new/redcapAPI.Rcheck/redcapAPI’ - -``` -### CRAN - -``` -* installing *source* package ‘redcapAPI’ ... -** package ‘redcapAPI’ successfully unpacked and MD5 sums checked -** libs -ccache clang -Qunused-arguments -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Rinit.c -o Rinit.o -ccache clang -Qunused-arguments -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o redcapAPI.so Rinit.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to /Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/redcapAPI/old/redcapAPI.Rcheck/redcapAPI/libs -** R -** inst -** preparing package for lazy loading -Error : object ‘[.labelled’ is not exported by 'namespace:Hmisc' -ERROR: lazy loading failed for package ‘redcapAPI’ -* removing ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/redcapAPI/old/redcapAPI.Rcheck/redcapAPI’ - -``` # reportRx Version: 1.0 @@ -5130,7 +5363,9 @@ Version: 1.2 * checking whether package ‘RGENERATEPREC’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘date’ was built under R version 3.4.3 Warning: package ‘MASS’ was built under R version 3.4.3 + Warning: package ‘zoo’ 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. ``` @@ -5149,7 +5384,7 @@ Version: 1.8 # RndTexExams -Version: 1.4 +Version: 1.4.1 ## In both @@ -5229,11 +5464,11 @@ Version: 1.10.0 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' + URL https://ftp.ncbi.nlm.nih.gov/geo/series/GSE4nnn/GSE4158/matrix//geo/series/GSE4nnn/GSE4158/: cannot open destfile '/tmp/RtmpvOd3Zv//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 + cannot open file '/tmp/RtmpvOd3Zv//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 @@ -5271,6 +5506,19 @@ Version: 1.10.0 to your NAMESPACE file. ``` +# rNOMADS + +Version: 2.3.9 + +## In both + +* checking whether package ‘rNOMADS’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘xml2’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/rNOMADS/new/rNOMADS.Rcheck/00install.out’ for details. + ``` + # rodham Version: 0.1.1 @@ -5311,7 +5559,7 @@ Version: 0.1.0 # RQGIS -Version: 1.0.2 +Version: 1.0.3 ## In both @@ -5342,6 +5590,38 @@ Version: 1.0.6 manual. ``` +# RSMET + +Version: 1.2.9 + +## Newly broken + +* checking examples ... ERROR + ``` + ... + > + > + > library(ggmap) + Loading required package: ggplot2 + > data(meteofranceSynop) + > + > + > + > + > data=meteofranceSynop[meteofranceSynop$timestamp==meteofranceSynop$timestamp[250],] + > + > + > + > map <- get_map(location ="France", zoom = 6) + Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false + Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false + Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France" + Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : + arguments imply differing number of rows: 0, 1 + Calls: get_map -> get_googlemap -> data.frame + Execution halted + ``` + # rsunlight Version: 0.4.2 @@ -5408,6 +5688,18 @@ Version: 1.3 All declared Imports should be used. ``` +# rubias + +Version: 0.1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘ggplot2’ + All declared Imports should be used. + ``` + # sasMap Version: 1.0.0 @@ -5486,7 +5778,7 @@ Version: 1.14.0 # Seurat -Version: 2.1.0 +Version: 2.2.0 ## In both @@ -5497,6 +5789,11 @@ Version: 2.1.0 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/Seurat/new/Seurat.Rcheck/00install.out’ for details. ``` +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘MetaDE’ + ``` + # ShinyItemAnalysis Version: 1.2.3 @@ -5522,6 +5819,7 @@ Version: 1.6.0 Found the following significant warnings: Warning: package ‘foreach’ was built under R version 3.4.3 Warning: package ‘iterators’ was built under R version 3.4.3 + Warning: package ‘matrixStats’ was built under R version 3.4.3 Warning: replacing previous import ‘plyr::count’ by ‘matrixStats::count’ when loading ‘SICtools’ See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/SICtools/new/SICtools.Rcheck/00install.out’ for details. ``` @@ -5603,11 +5901,24 @@ Version: 1.0.0 Package unavailable to check Rd xrefs: ‘sampling’ ``` +# simr + +Version: 1.0.3 + +## In both + +* checking whether package ‘simr’ 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/simr/new/simr.Rcheck/00install.out’ for details. + ``` + # sincell Version: 1.8.0 -## In both +## Newly broken * checking re-building of vignette outputs ... WARNING ``` @@ -5635,6 +5946,8 @@ Version: 1.8.0 Execution halted ``` +## In both + * checking R code for possible problems ... NOTE ``` ... @@ -5679,7 +5992,7 @@ Version: 1.8.0 # skimr -Version: 1.0 +Version: 1.0.1 ## In both @@ -5689,6 +6002,29 @@ Version: 1.0 All declared Imports should be used. ``` +# skynet + +Version: 1.0 + +## In both + +* checking dependencies in R code ... NOTE + ``` + Namespace in Imports field not imported from: ‘maps’ + All declared Imports should be used. + ``` + +# socialmixr + +Version: 0.1.1 + +## In both + +* checking data for non-ASCII characters ... NOTE + ``` + Note: found 1 marked UTF-8 string + ``` + # SomaticCancerAlterations Version: 1.12.0 @@ -5767,18 +6103,6 @@ Version: 0.6.0 All declared Imports should be used. ``` -# spind - -Version: 2.1.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘sp’ - All declared Imports should be used. - ``` - # sqlutils Version: 1.2 @@ -5862,7 +6186,7 @@ Version: 2.0-1 # stacomiR -Version: 0.5.3 +Version: 0.5.3.1 ## In both @@ -5929,6 +6253,52 @@ Version: 0.1.1 All declared Imports should be used. ``` +# stm + +Version: 1.3.3 + +## In both + +* checking package dependencies ... ERROR + ``` + Package required but not available: ‘quanteda’ + + See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ + manual. + ``` + +# stormwindmodel + +Version: 0.1.0 + +## Newly broken + +* checking re-building of vignette outputs ... WARNING + ``` + ... + + filter, lag + + The following objects are masked from 'package:base': + + intersect, setdiff, setequal, union + + + Attaching package: 'gridExtra' + + The following object is masked from 'package:dplyr': + + combine + + Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false + Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false + Warning: geocode failed with status OVER_QUERY_LIMIT, location = "georgia" + Quitting from lines 220-233 (Details.Rmd) + Error: processing vignette 'Details.Rmd' failed with diagnostics: + arguments imply differing number of rows: 0, 1 + Execution halted + ``` + # stplanr Version: 0.2.2 @@ -5974,7 +6344,7 @@ Version: 0.5.1 all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true. ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 8 SKIPPED: 0 FAILED: 1 + OK: 7 SKIPPED: 0 FAILED: 1 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) Error: testthat unit tests failed @@ -5989,9 +6359,9 @@ Version: 1.0.4 * checking installed package size ... NOTE ``` - installed size is 5.6Mb + installed size is 5.8Mb sub-directories of 1Mb or more: - R 1.8Mb + R 2.1Mb extdata 3.1Mb ``` @@ -6070,7 +6440,33 @@ Version: 0.1.1 Version: 2.5.9 -## Newly broken +## 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 tests ... ``` @@ -6078,7 +6474,7 @@ Version: 2.5.9 Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 112 SKIPPED: 0 FAILED: 16 + OK: 113 SKIPPED: 0 FAILED: 16 1. Error: TCGAanalyze_survival creates pdf (@test-analyse.R#4) 2. Error: Results from TCGAanalyze_DEA and DMR in starburst plot are correct (@test-analyse.R#182) 3. Error: GDCdownload API method for two files is working (@test-prepare-download.R#4) @@ -6120,44 +6516,6 @@ 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 @@ -6193,80 +6551,9 @@ Version: 2.5.9 visNet ``` -# TCGAbiolinksGUI - -Version: 1.2.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - ... - - The following objects are masked from 'package:S4Vectors': - - first, intersect, rename, setdiff, setequal, union - - The following objects are masked from 'package:BiocGenerics': - - combine, intersect, setdiff, union - - The following objects are masked from 'package:stats': - - filter, lag - - The following objects are masked from 'package:base': - - intersect, setdiff, setequal, union - - Quitting from lines 11-15 (data.Rmd) - Error: processing vignette 'data.Rmd' failed with diagnostics: - there is no package called 'DT' - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 30.3Mb - sub-directories of 1Mb or more: - app 1.0Mb - doc 28.9Mb - ``` - -* checking DESCRIPTION meta-information ... NOTE - ``` - Malformed Description field: should contain one or more complete sentences. - ``` - * checking for unstated dependencies in vignettes ... NOTE ``` - 'library' or 'require' calls not declared from: - ‘DT’ ‘dplyr’ - ``` - -# text2vec - -Version: 0.5.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.9Mb - sub-directories of 1Mb or more: - data 2.7Mb - doc 3.5Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘irlba’ - All declared Imports should be used. - ``` - -* checking for GNU extensions in Makefiles ... NOTE - ``` - GNU make is a SystemRequirements. + 'library' or 'require' call not declared from: ‘DT’ ``` # textreuse @@ -6311,30 +6598,33 @@ Version: 0.5.3 * checking whether package ‘tidyquant’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘zoo’ was built under R version 3.4.3 Warning: package ‘quantmod’ was built under R version 3.4.3 + Warning: package ‘TTR’ was built under R version 3.4.3 + Warning: package ‘tibble’ was built under R version 3.4.3 See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/tidyquant/new/tidyquant.Rcheck/00install.out’ for details. ``` * checking re-building of vignette outputs ... WARNING ``` ... + Warning in download.file(url, destfile = tmp, quiet = TRUE) : - cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' + URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': status was 'Couldn't resolve host name' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Warning in download.file(url, destfile = tmp, quiet = TRUE) : - cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' + URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': status was 'Couldn't resolve host name' Warning: x = 'AAPL', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=AAPL&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing AAPL. Warning in download.file(url, destfile = tmp, quiet = TRUE) : - cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' + URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': status was 'Couldn't resolve host name' Warning: x = 'FB', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=FB&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing FB. Warning in download.file(url, destfile = tmp, quiet = TRUE) : - cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': HTTP status was '403 Forbidden' + URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv': status was 'Couldn't resolve host name' Warning: x = 'GOOG', get = 'key.stats': Error in download.file(url, destfile = tmp, quiet = TRUE): cannot open URL 'http://download.finance.yahoo.com/d/quotes.csv?s=GOOG&f=aa2a5bb4b6c1c4dd1ee7e8e9f6ghjj1j2j4j5j6kk3k4k5ll1mm3m4m5m6m7m8nopp2p5p6qrr1r5r6r7s6s7t8vwxy&e=.csv' Removing GOOG. - Warning in value[[3L]](cond) : Returning as nested data frame. Quitting from lines 211-214 (TQ01-core-functions-in-tidyquant.Rmd) Error: processing vignette 'TQ01-core-functions-in-tidyquant.Rmd' failed with diagnostics: object 'Ask' not found @@ -6348,12 +6638,30 @@ Version: 0.5.3 All declared Imports should be used. ``` +# tidytext + +Version: 0.1.6 + +## In both + +* checking package dependencies ... NOTE + ``` + Packages suggested but not available for checking: ‘quanteda’ ‘stm’ + ``` + # tidyverse Version: 1.2.1 ## In both +* checking whether package ‘tidyverse’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘tibble’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/tidyverse/new/tidyverse.Rcheck/00install.out’ for details. + ``` + * checking dependencies in R code ... NOTE ``` Namespaces in Imports field not imported from: @@ -6616,13 +6924,6 @@ 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’ @@ -6689,7 +6990,7 @@ Version: 0.1.2 Version: 0.9.11 -## In both +## Newly broken * checking examples ... ERROR ``` @@ -6717,6 +7018,8 @@ Version: 0.9.11 Execution halted ``` +## In both + * checking whether package ‘vardpoor’ can be installed ... WARNING ``` Found the following significant warnings: @@ -6756,6 +7059,13 @@ Version: 1.3-28 ## In both +* checking whether package ‘vetools’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 + See ‘/Users/hadley/Documents/tidyverse/stringr/revdep/checks.noindex/vetools/new/vetools.Rcheck/00install.out’ for details. + ``` + * checking R code for possible problems ... NOTE ``` ... @@ -6792,6 +7102,7 @@ Version: 0.5 ``` Found the following significant warnings: Warning: package ‘lme4’ was built under R version 3.4.3 + Warning: package ‘mgcv’ 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. ``` @@ -6929,6 +7240,7 @@ Version: 2.2-1 * checking whether package ‘wux’ can be installed ... WARNING ``` Found the following significant warnings: + Warning: package ‘sp’ was built under R version 3.4.3 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. @@ -6950,36 +7262,68 @@ Version: 0.13.0 # xpose -Version: 0.4.0 +Version: 0.4.1 ## In both +* checking examples ... ERROR + ``` + ... + 2 2 T F + > + > # List output files data + > list_files(xpdb_ex_pk) + Files: + name extension problem subprob method data modified + + 1 run001.cor cor 1.00 0 foce F + 2 run001.cov cov 1.00 0 foce F + 3 run001.ext ext 1.00 0 foce F + 4 run001.grd grd 1.00 0 foce F + 5 run001.phi phi 1.00 0 foce F + 6 run001.shk shk 1.00 0 foce F + > + > # List special data + > xpdb_ex_pk %>% + + vpc_data(quiet = TRUE) %>% + + list_special() + Error in sim_cols$sim : $ operator is invalid for atomic vectors + Calls: %>% ... -> vpc_data -> -> add_sim_index_number + Execution halted + ``` + * checking tests ... ``` ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: - 9: equal_data_frame(target, current, ignore_col_order = ignore_col_order, ignore_row_order = ignore_row_order, - convert = convert) + ci = opt$ci, uloq = opt$uloq, lloq = opt$lloq, smooth = FALSE, vpcdb = TRUE, + verbose = !quiet) + 10: add_sim_index_number(sim, id = "id", sim_label = sim_cols$sim) ══ testthat results ═══════════════════════════════════════════════════════════ - 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) + OK: 423 SKIPPED: 4 FAILED: 6 + 1. Error: (unknown) (@test-console_outputs.R#4) + 2. Error: (unknown) (@test-edits.R#17) + 3. Failure: summary is properly created with the appropriate information (@test-model-summary.R#43) + 4. Failure: Termination messages are parsed when minimization is terminated (@test-model-summary.R#113) + 5. Error: (unknown) (@test-vpc.R#17) + 6. Error: (unknown) (@test-xpdb_access.R#4) Error: testthat unit tests failed Execution halted ``` -* checking dependencies in R code ... NOTE +* checking re-building of vignette outputs ... WARNING ``` - Namespace in Imports field not imported from: ‘gridExtra’ - All declared Imports should be used. + Error in re-building vignettes: + ... + Returning data from run001.ext, $prob no.1, subprob no.0, method foce + Returning parameter estimates from $prob no.1, subprob no.0, method foce + Quitting from lines 13-26 (customize_plots.Rmd) + Error: processing vignette 'customize_plots.Rmd' failed with diagnostics: + $ operator is invalid for atomic vectors + Execution halted ``` # ztype