diff --git a/cran-comments.md b/cran-comments.md index 3d8644f73..a41ed4113 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,4 +1,4 @@ -This is a small patch fixing test failures on CRAN +This release removes previously deprecated functions ## Test environments @@ -16,4 +16,17 @@ This is a small patch fixing test failures on CRAN ## Downstream dependencies -* I did not test all dependencies, but do not think any of the changes should effect them. +I ran `R CMD check` on all 316 reverse dependencies +(https://github.com/r-lib/devtools/tree/master/revdep) there were 6 regressions +detected. + +* available - submitted release 1.0.3 to fix the issue +* googleAuthR - sent PR https://github.com/MarkEdmondson1234/googleAuthR/pull/150 to fix the issue. +* packagedocs - sent PR https://github.com/hafen/packagedocs/pull/32 to fix the issue. +* soilcarbon - sent PR + https://github.com/powellcenter-soilcarbon/soilcarbon/pull/19 to remove the + devtools dependency, the issue also seems to have been already fixed in the + devel version of the package. +* understandBPMN - sent email to maintainer, patch to fix available at + https://github.com/cran/understandBPMN/compare/master...jimhester:remove-devtools.patch +* zebu - sent PR https://github.com/oliviermfmartin/zebu/pull/2 to remove the devtools dependency diff --git a/revdep/README.md b/revdep/README.md index 6b94ef5e8..c122290c2 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -2,397 +2,57 @@ |field |value | |:--------|:----------------------------| -|version |R version 3.5.1 (2018-07-02) | -|os |macOS 10.14 | +|version |R version 3.6.0 (2019-04-26) | +|os |macOS Mojave 10.14.4 | |system |x86_64, darwin15.6.0 | |ui |X11 | |language |(EN) | |collate |en_US.UTF-8 | |ctype |en_US.UTF-8 | |tz |America/New_York | -|date |2018-10-09 | +|date |2019-07-01 | # Dependencies -|package |old |new |Δ | -|:-----------|:------|:-----------|:--| -|devtools |1.13.6 |1.13.6.9000 |* | -|assertthat |NA |0.2.0 |* | -|backports |NA |1.1.2 |* | -|base64enc |NA |0.1-3 |* | -|callr |NA |3.0.0 |* | -|cli |NA |1.0.1 |* | -|clipr |NA |0.4.1 |* | -|clisymbols |NA |1.2.0 |* | -|crayon |NA |1.3.4 |* | -|curl |3.2 |3.2 | | -|desc |NA |1.2.0 |* | -|digest |0.6.17 |0.6.17 | | -|fs |NA |1.2.6 |* | -|gh |NA |1.0.1 |* | -|git2r |0.23.0 |0.23.0 | | -|glue |NA |1.3.0 |* | -|httr |1.3.1 |1.3.1 | | -|ini |NA |0.3.1 |* | -|jsonlite |1.5 |1.5 | | -|magrittr |NA |1.5 |* | -|memoise |1.1.0 |1.1.0 | | -|mime |0.6 |0.6 | | -|openssl |1.0.2 |1.0.2 | | -|pkgbuild |NA |1.0.1 |* | -|pkgload |NA |1.0.0 |* | -|prettyunits |NA |1.0.2 |* | -|processx |NA |3.2.0 |* | -|ps |NA |1.1.0 |* | -|R6 |2.3.0 |2.3.0 | | -|rcmdcheck |NA |1.3.0 |* | -|Rcpp |NA |0.12.19 |* | -|remotes |NA |1.1.1.9000 |* | -|rlang |NA |0.2.2 |* | -|rprojroot |NA |1.3-2 |* | -|rstudioapi |0.8 |0.8 | | -|sessioninfo |NA |1.1.0 |* | -|usethis |NA |1.4.0 |* | -|whisker |0.3-2 |0.3-2 | | -|withr |2.1.2 |2.1.2 | | -|xopen |NA |1.0.0 |* | +|package |old |new |Δ | +|:--------|:-----|:------|:--| +|devtools |2.0.2 |2.1.0 |* | +|git2r |NA |0.26.1 |* | +|mime |NA |0.7 |* | +|praise |NA |1.0.0 |* | +|remotes |NA |2.1.0 |* | +|rlang |NA |0.4.0 |* | +|testthat |NA |2.1.1 |* | # Revdeps -## Couldn't check (5) - -|package |version |error |warning |note | -|:------------------------------------------------------|:-------|:------|:-------|:----| -|[microsamplingDesign](problems.md#microsamplingdesign) |1.0.5 |__+1__ | | | -|[PSPManalysis](problems.md#pspmanalysis) |0.2.0 |__+1__ | | | -|[recount](problems.md#recount) |1.6.3 |1 | |3 | -|[segclust2d](problems.md#segclust2d) |0.1.0 |1 | | | -|[TCGAbiolinks](problems.md#tcgabiolinks) |2.8.4 |1 |1 |2 | - -## Broken (14) - -|package |version |error |warning |note | -|:---------------------------------------------------|:-------|:------|:-------|:--------| -|[assertive.code](problems.md#assertivecode) |0.0-1 |__+1__ | | | -|[assertive.data](problems.md#assertivedata) |0.0-1 |__+1__ | | | -|[assertive.data.uk](problems.md#assertivedatauk) |0.0-1 |__+1__ | | | -|[assertive.data.us](problems.md#assertivedataus) |0.0-1 |__+1__ | | | -|[assertive.matrices](problems.md#assertivematrices) |0.0-1 |__+1__ | |1 | -|[assertive.models](problems.md#assertivemodels) |0.0-1 |__+1__ | | | -|[BiocWorkflowTools](problems.md#biocworkflowtools) |1.6.2 | |__+1__ |2 | -|[fakemake](problems.md#fakemake) |1.3.0 | |__+2__ |-1 | -|[icd9](problems.md#icd9) |1.3.1 | | |1 __+1__ | -|[msgtools](problems.md#msgtools) |0.2.7 | |__+1__ | | -|[pacman](problems.md#pacman) |0.4.6 |__+1__ | | | -|[spectrolab](problems.md#spectrolab) |0.0.7 | |__+1__ |1 | -|[testthat](problems.md#testthat) |2.0.0 |__+1__ | | | -|[unitizer](problems.md#unitizer) |1.4.5 |__+1__ | | | - -## All (303) - -|package |version |error |warning |note | -|:------------------------------------------------------------------|:-------------|:------|:-------|:--------| -|[abjutils](problems.md#abjutils) |0.2.1 | | |1 | -|acmeR |1.1.0 | | | | -|ActisoftR |0.0.1 | | | | -|[adapr](problems.md#adapr) |2.0.0 | | |1 | -|adaptalint |0.2.3 | | | | -|addinslist |0.2 | | | | -|alluvial |0.1-2 | | | | -|[alphavantager](problems.md#alphavantager) |0.1.0 |1 | |1 | -|[aMNLFA](problems.md#amnlfa) |0.1 | | |1 | -|[amt](problems.md#amt) |0.0.5.0 | | |1 | -|[annotatr](problems.md#annotatr) |1.6.0 |1 |1 |2 | -|[anomalize](problems.md#anomalize) |0.1.1 | | |1 | -|[anyLib](problems.md#anylib) |1.0.4 | | |1 | -|[archivist](problems.md#archivist) |2.3.1 | | |2 | -|aRxiv |0.5.16 | | | | -|[assertive.code](problems.md#assertivecode) |0.0-1 |__+1__ | | | -|[assertive.data](problems.md#assertivedata) |0.0-1 |__+1__ | | | -|[assertive.data.uk](problems.md#assertivedatauk) |0.0-1 |__+1__ | | | -|[assertive.data.us](problems.md#assertivedataus) |0.0-1 |__+1__ | | | -|[assertive.matrices](problems.md#assertivematrices) |0.0-1 |__+1__ | |1 | -|[assertive.models](problems.md#assertivemodels) |0.0-1 |__+1__ | | | -|[AUCell](problems.md#aucell) |1.2.4 | | |5 | -|automagic |0.3 | | | | -|available |1.0.1 | | | | -|ballr |0.2.1 | | | | -|[baytrends](problems.md#baytrends) |1.0.7 | | |1 | -|[BEACH](problems.md#beach) |1.2.1 | | |1 | -|[beachmat](problems.md#beachmat) |1.2.1 | | |1 | -|[BETS](problems.md#bets) |0.4.4 | | |1 | -|[bigstep](problems.md#bigstep) |1.0.0 | | |1 | -|[BiocCheck](problems.md#bioccheck) |1.16.0 | |1 |3 | -|[BiocWorkflowTools](problems.md#biocworkflowtools) |1.6.2 | |__+1__ |2 | -|[BioInstaller](problems.md#bioinstaller) |0.3.6 |1 | |1 | -|biomartr |0.8.0 | | | | -|biospear |1.0.1 | | | | -|bisectr |0.1.0 | | | | -|[biwavelet](problems.md#biwavelet) |0.20.17 | | |1 | -|[BloodCancerMultiOmics2017](problems.md#bloodcancermultiomics2017) |1.0.2 | |1 |3 | -|[BrailleR](problems.md#brailler) |0.29.1 | | |1 | -|broman |0.68-2 | | | | -|BUMHMM |1.4.0 | | | | -|[cartools](problems.md#cartools) |0.1.0 | | |1 | -|[CGPfunctions](problems.md#cgpfunctions) |0.4 | | |2 | -|checkmate |1.8.5 | | | | -|ChemometricsWithR |0.1.11 | | | | -|[chimeraviz](problems.md#chimeraviz) |1.6.1 |1 | | | -|[chipenrich](problems.md#chipenrich) |2.4.0 |1 | | | -|[chipenrich.data](problems.md#chipenrichdata) |2.4.0 | | |2 | -|chromswitch |1.2.1 | | | | -|[civis](problems.md#civis) |1.5.1 | | |1 | -|CluMix |2.1 | | | | -|[ClusterJudge](problems.md#clusterjudge) |1.2.0 |1 |1 |1 | -|[codemetar](problems.md#codemetar) |0.1.6 | | |1 | -|codyn |2.0.0 | | | | -|[cogena](problems.md#cogena) |1.14.0 | |1 |3 | -|[COMPASS](problems.md#compass) |1.18.0 | |1 |3 | -|[CompGLM](problems.md#compglm) |2.0 |1 | | | -|[congressbr](problems.md#congressbr) |0.1.3 | | |1 | -|constellation |0.2.0 | | | | -|CorShrink |0.1-6 | | | | -|[CountClust](problems.md#countclust) |1.8.0 | | |1 | -|creditr |0.6.1 | | | | -|[crunch](problems.md#crunch) |1.24.0 | | |1 | -|[curatedMetagenomicData](problems.md#curatedmetagenomicdata) |1.10.2 | | |1 | -|DataCombine |0.2.21 | | | | -|DataPackageR |0.15.3 | | | | -|datr |0.1.0 | | | | -|DCG |0.9.2 | | | | -|deBInfer |0.4.2 | | | | -|[demi](problems.md#demi) |1.1.2 | | |1 | -|[derfinder](problems.md#derfinder) |1.14.0 |1 |1 |4 | -|[derfinderData](problems.md#derfinderdata) |0.114.0 | | |1 | -|[derfinderHelper](problems.md#derfinderhelper) |1.14.0 | |1 |1 | -|[derfinderPlot](problems.md#derfinderplot) |1.14.0 |2 |1 |2 | -|diffdf |1.0.1 | | | | -|[DLMtool](problems.md#dlmtool) |5.2.3 | | |1 | -|docstring |1.0.0 | | | | -|document |3.0.2 | | | | -|[dodgr](problems.md#dodgr) |0.0.3 | |1 | | -|doremi |0.1.0 | |-1 | | -|[doRNG](problems.md#dorng) |1.7.1 | | |2 | -|dparser |0.1.8 | | | | -|dpmr |0.1.9 | | | | -|dr4pl |1.1.7.1 | | | | -|DrImpute |1.0 | | | | -|[dynutils](problems.md#dynutils) |1.0.0 | | |1 | -|easypackages |0.1.0 | | | | -|edgarWebR |1.0.0 | | | | -|[elementR](problems.md#elementr) |1.3.6 |1 | |1 | -|[ELMER.data](problems.md#elmerdata) |2.4.2 | | |4 | -|[epiNEM](problems.md#epinem) |1.4.0 | |1 |3 | -|episode |1.0.0 | | | | -|etl |0.3.7 | | | | -|[EValue](problems.md#evalue) |1.1.5 | | |1 | -|exampletestr |1.4.0 | | | | -|[excerptr](problems.md#excerptr) |1.4.1 |2 | | | -|[ExPanDaR](problems.md#expandar) |0.2.0 | | |1 | -|[fakemake](problems.md#fakemake) |1.3.0 | |__+2__ |-1 | -|FedData |2.5.5 | | | | -|[fitODBOD](problems.md#fitodbod) |1.2.0 | | |1 | -|flacco |1.7 | | | | -|flippant |1.1.0 | | | | -|FossilSim |2.0.0 | | | | -|ganalytics |0.10.4 | | | | -|[gbfs](problems.md#gbfs) |1.0.0 | |1 |1 | -|getTBinR |0.5.4 | | | | -|ggalluvial |0.9.0 | | | | -|[ggExtra](problems.md#ggextra) |0.8 | | |1 | -|ggforce |0.1.3 | | | | -|ggrepel |0.8.0 | | | | -|[githubinstall](problems.md#githubinstall) |0.2.2 | | |1 | -|gitlabr |0.9 | | | | -|[googleAuthR](problems.md#googleauthr) |0.6.3 | | |1 | -|googleComputeEngineR |0.2.0 | | | | -|graticule |0.1.2 | | | | -|[gsrc](problems.md#gsrc) |1.1 | |1 |1 | -|hashmap |0.2.2 | | | | -|heuristica |1.0.1 | | | | -|[HMP16SData](problems.md#hmp16sdata) |1.0.1 | |1 |2 | -|HURDAT |0.2.0 | | | | -|huxtable |4.1.0 | | | | -|[hyperSpec](problems.md#hyperspec) |0.99-20180627 | | |2 | -|IalsaSynthesis |0.1.6 | | | | -|[icd9](problems.md#icd9) |1.3.1 | | |1 __+1__ | -|[IHW](problems.md#ihw) |1.8.0 | |1 |3 | -|[iLaplace](problems.md#ilaplace) |1.1.0 | |1 | | -|iml |0.7.0 | | | | -|infer |0.3.1 | | | | -|inlmisc |0.4.3 | | | | -|IPtoCountry |0.0.1 | | | | -|jetpack |0.3.1 | | | | -|jiebaR |0.9.99 | | | | -|JWileymisc |0.3.1 | | | | -|konfound |0.1.0 | | | | -|[KoNLP](problems.md#konlp) |0.80.1 | | |1 | -|LAGOSNE |1.1.0 | | | | -|latticeDensity |1.1.0 | | | | -|learnrbook |0.0.2 | | | | -|letsR |3.1 | | | | -|librarian |1.3.0 | | | | -|[likert](problems.md#likert) |1.3.5 | | |1 | -|[lilikoi](problems.md#lilikoi) |0.1.0 | | |3 | -|[lime](problems.md#lime) |0.4.0 |1 | | | -|lineup |0.37-10 | | | | -|lmQCM |0.1.2 | | | | -|Logolas |1.4.0 | | | | -|[loose.rock](problems.md#looserock) |1.0.9 | | |1 | -|[Luminescence](problems.md#luminescence) |0.8.5 | | |1 | -|manifestoR |1.3.0 | | | | -|[MCbiclust](problems.md#mcbiclust) |1.4.0 |1 | | | -|mcglm |0.4.0 | | | | -|[metafolio](problems.md#metafolio) |0.1.0 | | |1 | -|[metagenomeFeatures](problems.md#metagenomefeatures) |2.0.0 | |2 |2 | -|mgarchBEKK |0.0.2 | | | | -|[micompr](problems.md#micompr) |1.1.0 |2 |1 |2 | -|[microsamplingDesign](problems.md#microsamplingdesign) |1.0.5 |__+1__ | | | -|miniCRAN |0.2.11 | | | | -|miscset |1.1.0 | | | | -|mixchar |0.1.0 | | | | -|[MODIS](problems.md#modis) |1.1.3 | |4 |3 | -|modules |0.7.0 | | | | -|Momocs |1.2.9 | | | | -|[MonetDBLite](problems.md#monetdblite) |0.6.0 | | |1 | -|[MoonlightR](problems.md#moonlightr) |1.6.1 | | |1 | -|morpheus |0.2-0 | | | | -|mptools |1.0.1 | | | | -|[msgtools](problems.md#msgtools) |0.2.7 | |__+1__ | | -|[myTAI](problems.md#mytai) |0.8.0 | | |2 | -|[networktools](problems.md#networktools) |1.2.0 | | |1 | -|[nima](problems.md#nima) |0.5.0 | | |1 | -|nlmixr |0.9.1-3 | | | | -|[NlsyLinks](problems.md#nlsylinks) |2.0.6 | | |1 | -|[NMF](problems.md#nmf) |0.21.0 | | |2 | -|[npsm](problems.md#npsm) |0.5 | | |1 | -|[opencpu](problems.md#opencpu) |2.0.8 | | |1 | -|[OpenMx](problems.md#openmx) |2.11.3 | | |3 | -|[openPrimeR](problems.md#openprimer) |1.2.0 | | |2 | -|[OPWeight](problems.md#opweight) |1.2.0 | |1 |1 | -|Orcs |1.0.0 | | | | -|osmdata |0.0.7 | | | | -|[osmplotr](problems.md#osmplotr) |0.3.0 | | |1 | -|OSTSC |0.0.1 | | | | -|packagedocs |0.4.0 | | | | -|[packrat](problems.md#packrat) |0.4.9-3 | | |1 | -|[pacman](problems.md#pacman) |0.4.6 |__+1__ | | | -|[parlitools](problems.md#parlitools) |0.2.1 | | |1 | -|PathoStat |1.6.1 | | | | -|pcr |1.1.2 | | | | -|Perc |0.1.2 | | | | -|performanceEstimation |1.1.0 | | | | -|[pkgdown](problems.md#pkgdown) |1.1.0 |1 | | | -|[pkgmaker](problems.md#pkgmaker) |0.27 | | |1 | -|[pkgnet](problems.md#pkgnet) |0.2.0 | | |1 | -|[PKPDmisc](problems.md#pkpdmisc) |2.1.1 | | |1 | -|[plotly](problems.md#plotly) |4.8.0 | | |1 | -|[poio](problems.md#poio) |0.0-3 | | |2 | -|populationPDXdesign |1.0.3 | | | | -|princurve |2.1.2.1 | | | | -|[prodigenr](problems.md#prodigenr) |0.4.0 | | |1 | -|profvis |0.3.5 | | | | -|[PSAboot](problems.md#psaboot) |1.1.4 | | |1 | -|[psichomics](problems.md#psichomics) |1.6.1 | | |3 | -|[PSPManalysis](problems.md#pspmanalysis) |0.2.0 |__+1__ | | | -|[pulver](problems.md#pulver) |0.1.0 |1 | | | -|[qqplotr](problems.md#qqplotr) |0.0.3 | | |1 | -|[qsort](problems.md#qsort) |0.2.2 | | |1 | -|qtlcharts |0.9-6 | | | | -|qwraps2 |0.3.0 | | | | -|radiomics |0.1.3 | | | | -|raw |0.1.6 | | | | -|[rbundler](problems.md#rbundler) |0.3.7 | | |2 | -|Rcereal |1.2.1 | | | | -|[RcppProgress](problems.md#rcppprogress) |0.4.1 |1 | | | -|RCzechia |1.3.0 | | | | -|Rd2md |0.0.2 | | | | -|rddapp |1.1.0 | | | | -|rdoxygen |1.0.0 | | | | -|readit |1.0.0 | | | | -|recexcavAAR |0.3.0 | | | | -|[recount](problems.md#recount) |1.6.3 |1 | |3 | -|REDCapR |0.9.8 | | | | -|redlistr |1.0.1 | | | | -|[regionReport](problems.md#regionreport) |1.14.3 |1 |1 |2 | -|[reprex](problems.md#reprex) |0.2.1 | | |1 | -|[reproducible](problems.md#reproducible) |0.2.3 | | |1 | -|[rfishbase](problems.md#rfishbase) |2.1.2 | | |1 | -|[Ricetl](problems.md#ricetl) |0.2.5 |1 | | | -|Rilostat |0.2.1 | | | | -|riskyr |0.1.0 | | | | -|[RIVER](problems.md#river) |1.4.0 | | |1 | -|[rnaturalearth](problems.md#rnaturalearth) |0.1.0 | | |2 | -|robustBLME |0.1.3 | | | | -|ropenaq |0.2.6 | | | | -|roxygen2 |6.1.0 | | | | -|[rpivotTable](problems.md#rpivottable) |0.3.0 | | |1 | -|[rsimsum](problems.md#rsimsum) |0.3.3 | | |1 | -|[rsMove](problems.md#rsmove) |0.2.4 | | |1 | -|[rsoi](problems.md#rsoi) |0.3.0 | | |1 | -|rstantools |1.5.1 | | | | -|RSuite |0.32-244 | | | | -|[RTCGA](problems.md#rtcga) |1.10.0 |2 | |3 | -|[RtutoR](problems.md#rtutor) |1.2 | | |1 | -|RxODE |0.7.2-5 | | | | -|[Ryacas](problems.md#ryacas) |0.3-1 | |1 | | -|satellite |1.0.1 | | | | -|[SciencesPo](problems.md#sciencespo) |1.4.1 | |1 |1 | -|SCnorm |1.2.1 | | | | -|scriptName |1.0.0 | | | | -|[segclust2d](problems.md#segclust2d) |0.1.0 |1 | | | -|smss |1.0-2 | | | | -|[soilcarbon](problems.md#soilcarbon) |1.2.0 | | |1 | -|[SpaDES](problems.md#spades) |2.0.2 |1 | | | -|[SpaDES.addins](problems.md#spadesaddins) |0.1.1 |1 | | | -|spduration |0.17.1 | | | | -|[specmine](problems.md#specmine) |2.0.3 | | |1 | -|[spectrolab](problems.md#spectrolab) |0.0.7 | |__+1__ |1 | -|[spew](problems.md#spew) |1.3.0 | |1 |2 | -|[SpidermiR](problems.md#spidermir) |1.10.0 |1 | | | -|spotGUI |0.2.0 | | | | -|srnadiff |1.0.0 | | | | -|[StarBioTrek](problems.md#starbiotrek) |1.6.0 |1 | | | -|stremr |0.4 | | | | -|SuperLearner |2.0-24 | | | | -|[sweep](problems.md#sweep) |0.2.1.1 | | |1 | -|[syuzhet](problems.md#syuzhet) |1.0.4 | | |1 | -|[taxlist](problems.md#taxlist) |0.1.5 | | |2 | -|[TCGAbiolinks](problems.md#tcgabiolinks) |2.8.4 |1 |1 |2 | -|[TCGAbiolinksGUI](problems.md#tcgabiolinksgui) |1.6.1 |1 | | | -|[TCGAutils](problems.md#tcgautils) |1.0.1 | |1 |2 | -|teachingApps |1.0.4 | | | | -|[testthat](problems.md#testthat) |2.0.0 |__+1__ | | | -|testthis |1.0.4 | | | | -|TeXCheckR |0.6.0 | | | | -|[texmex](problems.md#texmex) |2.4 | | |1 | -|thinkr |0.13 | | | | -|tidyLPA |0.2.0 | | | | -|[timetk](problems.md#timetk) |0.1.1.1 | | |1 | -|tinyProject |0.5 | | | | -|[tosca](problems.md#tosca) |0.1-2 | | |2 | -|[toxplot](problems.md#toxplot) |0.1.1 | | |1 | -|Trendy |1.2.9 |-1 | | | -|TSstudio |0.1.1 | | | | -|[twoddpcr](problems.md#twoddpcr) |1.4.1 | | |1 | -|uavRmp |0.5.3 | | | | -|[UKgrid](problems.md#ukgrid) |0.1.0 | | |2 | -|[umx](problems.md#umx) |2.8.0 | | |2 | -|understandBPMN |1.1.0 | | | | -|[unitizer](problems.md#unitizer) |1.4.5 |__+1__ | | | -|[unvotes](problems.md#unvotes) |0.2.0 | | |1 | -|valr |0.4.1 | | | | -|vdiffr |0.2.3 | | | | -|[veccompare](problems.md#veccompare) |0.1.0 | | |1 | -|[vegtable](problems.md#vegtable) |0.1.3 | | |1 | -|vortexR |1.1.5 | | | | -|[Wats](problems.md#wats) |0.10.3 | | |1 | -|[weathercan](problems.md#weathercan) |0.2.7 | | |1 | -|webTRISr |0.1.0 | | | | -|wikipediatrend |1.1.14 | | | | -|[workflowr](problems.md#workflowr) |1.1.1 |1 | | | -|[wru](problems.md#wru) |0.1-7 | | |1 | -|xoi |0.67-4 | | | | -|yearn |0.1.3 | | | | -|zebu |0.1.2 | | | | +## Failed to check (13) + +|package |version |error |warning |note | +|:-------------------------------------|:-------|:-----|:-------|:------| +|clustermq |0.8.8 |1 | |1 | +|ctsem |2.9.6 |1 | |2 | +|FoldGO |1.2.0 |1 | | | +|infer |0.4.0.1 |1 | | | +|jwutil |1.2.3 |1 | | | +|lilikoi |0.1.0 |1 | |2 | +|link2GI |0.3-5 |1 | | | +|mnem |1.0.0 |1 | | | +|MoonlightR |1.10.0 |1 | | | +|[SpaDES.core](failures.md#spadescore) |0.2.5 |2 | |__+1__ | +|StarBioTrek |1.10.0 |1 | | | +|TCGAbiolinks |2.12.2 |1 |2 |4 | +|TCGAbiolinksGUI |1.10.0 |1 | | | + +## New problems (7) + +|package |version |error |warning |note | +|:--------------------------------------------------|:-------|:-----|:-------|:--------| +|[available](problems.md#available) |1.0.2 | | |1 __+1__ | +|[BiocWorkflowTools](problems.md#biocworkflowtools) |1.10.0 | |__+1__ |1 | +|[googleAuthR](problems.md#googleauthr) |0.8.0 | |__+1__ |1 | +|[packagedocs](problems.md#packagedocs) |0.4.0 | | |__+1__ | +|[soilcarbon](problems.md#soilcarbon) |1.2.0 | | |1 __+1__ | +|[understandBPMN](problems.md#understandbpmn) |1.1.0 | | |__+1__ | +|[zebu](problems.md#zebu) |0.1.2 | | |__+1__ | diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 000000000..31dd36948 --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1,1234 @@ +# clustermq + +
+ +* Version: 0.8.8 +* Source code: https://github.com/cran/clustermq +* URL: https://github.com/mschubert/clustermq +* BugReports: https://github.com/mschubert/clustermq/issues +* Date/Publication: 2019-06-05 22:00:39 UTC +* Number of recursive dependencies: 74 + +Run `revdep_details(,"clustermq")` for more info + +
+ +## In both + +* R CMD check timed out + + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘R6’ ‘purrr’ + All declared Imports should be used. + ``` + +# ctsem + +
+ +* Version: 2.9.6 +* Source code: https://github.com/cran/ctsem +* URL: https://github.com/cdriveraus/ctsem +* Date/Publication: 2019-05-29 13:40:09 UTC +* Number of recursive dependencies: 103 + +Run `revdep_details(,"ctsem")` for more info + +
+ +## In both + +* R CMD check timed out + + +* checking installed package size ... NOTE + ``` + installed size is 10.4Mb + sub-directories of 1Mb or more: + R 2.0Mb + data 1.8Mb + libs 5.5Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘ggplot2’ ‘pkgbuild’ + All declared Imports should be used. + ``` + +# FoldGO + +
+ +* Version: 1.2.0 +* Source code: https://github.com/cran/FoldGO +* Date/Publication: 2019-05-02 +* Number of recursive dependencies: 104 + +Run `revdep_details(,"FoldGO")` for more info + +
+ +## In both + +* checking whether package ‘FoldGO’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/FoldGO/new/FoldGO.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘FoldGO’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘down_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘down_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘up_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘up_annotobj’ +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘GO.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘FoldGO’ +* removing ‘.../revdep/checks.noindex/FoldGO/new/FoldGO.Rcheck/FoldGO’ + +``` +### CRAN + +``` +* installing *source* package ‘FoldGO’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘down_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘down_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘up_annotobj’ +Warning: namespace ‘topGO’ is not available and has been replaced +by .GlobalEnv when processing object ‘up_annotobj’ +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘GO.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘FoldGO’ +* removing ‘.../revdep/checks.noindex/FoldGO/old/FoldGO.Rcheck/FoldGO’ + +``` +# infer + +
+ +* Version: 0.4.0.1 +* Source code: https://github.com/cran/infer +* URL: https://github.com/tidymodels/infer +* BugReports: https://github.com/tidymodels/infer/issues +* Date/Publication: 2019-04-22 06:58:08 UTC +* Number of recursive dependencies: 89 + +Run `revdep_details(,"infer")` for more info + +
+ +## In both + +* R CMD check timed out + + +# jwutil + +
+ +* Version: 1.2.3 +* Source code: https://github.com/cran/jwutil +* URL: https://github.com/jackwasey/jwutil +* BugReports: https://github.com/jackwasey/jwutil/issues +* Date/Publication: 2019-05-06 19:10:03 UTC +* Number of recursive dependencies: 52 + +Run `revdep_details(,"jwutil")` for more info + +
+ +## In both + +* checking whether package ‘jwutil’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/jwutil/new/jwutil.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘jwutil’ ... +** package ‘jwutil’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c RcppExports.cpp -o RcppExports.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c get_current_stdlib.cpp -o get_current_stdlib.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c jwomp.cpp -o jwomp.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c rowsorted.cpp -o rowsorted.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c stdlib.cpp -o stdlib.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c test-jwutil.cpp -o test-jwutil.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c test-runner.cpp -o test-runner.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/devtools/new/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c util.cpp -o util.o +clang: error: unsupported option '-fopenmp' +make: *** [get_current_stdlib.o] Error 1 +clang: make: *** Waiting for unfinished jobs.... +error: unsupported option '-fopenmp' +clang: error: unsupported option '-fopenmp' +clang: error: unsupported option '-fopenmp' +make: *** [stdlib.o] Error 1 +make: *** [RcppExports.o] Error 1 +make: *** [rowsorted.o] Error 1 +clang: error: unsupported option '-fopenmp' +make: *** [jwomp.o] Error 1 +clang: error: unsupported option '-fopenmp' +make: *** [test-jwutil.o] Error 1 +clang: error: unsupported option '-fopenmp' +clang: error: unsupported option '-fopenmp' +make: *** [test-runner.o] Error 1 +make: *** [util.o] Error 1 +ERROR: compilation failed for package ‘jwutil’ +* removing ‘.../revdep/checks.noindex/jwutil/new/jwutil.Rcheck/jwutil’ + +``` +### CRAN + +``` +* installing *source* package ‘jwutil’ ... +** package ‘jwutil’ successfully unpacked and MD5 sums checked +** using staged installation +** libs +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c RcppExports.cpp -o RcppExports.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c get_current_stdlib.cpp -o get_current_stdlib.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c jwomp.cpp -o jwomp.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c rowsorted.cpp -o rowsorted.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c stdlib.cpp -o stdlib.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c test-jwutil.cpp -o test-jwutil.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c test-runner.cpp -o test-runner.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/jwutil/Rcpp/include" -I".../revdep/library.noindex/jwutil/testthat/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -I. -fopenmp -fPIC -g -O0 -Wall -pedantic -fdiagnostics-color=always -Wsign-compare -march=native -c util.cpp -o util.o +clang: error: unsupported option '-fopenmp' +clang: error: unsupported option '-fopenmp' +clang: error: unsupported option '-fopenmp' +clang: error: make: *** [test-jwutil.o] Error 1 +make: *** Waiting for unfinished jobs.... +make: *** [get_current_stdlib.o] Error 1 +unsupported option '-fopenmp' +clangmake: *** [rowsorted.o] Error 1 +: error: unsupported option '-fopenmp' +make: *** [jwomp.o] Error 1 +clang: error: unsupported option '-fopenmp' +make: *** [stdlib.o] Error 1 +make: *** [RcppExports.o] Error 1 +clang: error: unsupported option '-fopenmp' +make: *** [test-runner.o] Error 1 +clang: error: unsupported option '-fopenmp' +make: *** [util.o] Error 1 +ERROR: compilation failed for package ‘jwutil’ +* removing ‘.../revdep/checks.noindex/jwutil/old/jwutil.Rcheck/jwutil’ + +``` +# lilikoi + +
+ +* Version: 0.1.0 +* Source code: https://github.com/cran/lilikoi +* URL: https://github.com/lanagarmire/lilikoi +* BugReports: https://github.com/lanagarmire/lilikoi/issues +* Date/Publication: 2018-07-30 11:10:03 UTC +* Number of recursive dependencies: 130 + +Run `revdep_details(,"lilikoi")` for more info + +
+ +## In both + +* R CMD check timed out + + +* checking installed package size ... NOTE + ``` + installed size is 5.4Mb + sub-directories of 1Mb or more: + data 4.1Mb + extdata 1.1Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + Namespaces in Imports field not imported from: + ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’ + All declared Imports should be used. + ``` + +# link2GI + +
+ +* Version: 0.3-5 +* Source code: https://github.com/cran/link2GI +* Date/Publication: 2018-10-26 23:00:03 UTC +* Number of recursive dependencies: 89 + +Run `revdep_details(,"link2GI")` for more info + +
+ +## In both + +* R CMD check timed out + + +# mnem + +
+ +* Version: 1.0.0 +* Source code: https://github.com/cran/mnem +* Date/Publication: 2019-05-02 +* Number of recursive dependencies: 142 + +Run `revdep_details(,"mnem")` for more info + +
+ +## In both + +* checking whether package ‘mnem’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/mnem/new/mnem.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘mnem’ ... +** using staged installation +** libs +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/mnem/Rcpp/include" -I".../revdep/library.noindex/mnem/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -O3 -c RcppExports.cpp -o RcppExports.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/mnem/Rcpp/include" -I".../revdep/library.noindex/mnem/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -O3 -c mm.cpp -o mm.o +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:1: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Core:535: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:2: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/LU:47: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:12: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Jacobi:29: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/QR:17: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Householder:27: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SVD:48: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:6: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Geometry:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:7: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Eigenvalues:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:26: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCore:66: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:27: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/OrderingMethods:71: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:29: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseQR:35: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:33: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/CholmodSupport:45: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:35: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:39: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/Polynomials:135: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:40: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:1: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Core:535: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:2: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/LU:47: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:12: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Jacobi:29: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/QR:17: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Householder:27: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SVD:48: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:6: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Geometry:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:7: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Eigenvalues:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:26: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCore:66: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:27: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/OrderingMethods:71: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:29: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseQR:35: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:33: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/CholmodSupport:45: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:35: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:39: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/Polynomials:135: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:40: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +clang++ -std=gnu++11 -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 mnem.so RcppExports.o mm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +installing to .../revdep/checks.noindex/mnem/new/mnem.Rcheck/00LOCK-mnem/00new/mnem/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘pcalg’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘mnem’ +* removing ‘.../revdep/checks.noindex/mnem/new/mnem.Rcheck/mnem’ + +``` +### CRAN + +``` +* installing *source* package ‘mnem’ ... +** using staged installation +** libs +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/mnem/Rcpp/include" -I".../revdep/library.noindex/mnem/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -O3 -c RcppExports.cpp -o RcppExports.o +clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/mnem/Rcpp/include" -I".../revdep/library.noindex/mnem/RcppEigen/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -O3 -c mm.cpp -o mm.o +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:1: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Core:535: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:2: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/LU:47: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:12: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Jacobi:29: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/QR:17: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Householder:27: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SVD:48: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:6: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Geometry:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:7: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Eigenvalues:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:26: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCore:66: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:27: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/OrderingMethods:71: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:29: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseQR:35: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:33: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/CholmodSupport:45: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:35: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:39: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/Polynomials:135: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from RcppExports.cpp:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:40: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:1: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Core:535: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:2: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/LU:47: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:12: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Jacobi:29: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:3: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Cholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:4: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/QR:17: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Householder:27: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SVD:48: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:6: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Geometry:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:30: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Dense:7: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Eigenvalues:58: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:26: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCore:66: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:27: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/OrderingMethods:71: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:29: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseCholesky:43: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/SparseQR:35: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:31: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/Sparse:33: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/IterativeLinearSolvers:46: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:32: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/Eigen/CholmodSupport:45: +.../revdep/library.noindex/mnem/RcppEigen/include/Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:35: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/KroneckerProduct:34: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:39: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/Polynomials:135: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +In file included from mm.cpp:5: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigen.h:25: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/RcppEigenForward.h:40: +In file included from .../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/SparseExtra:51: +.../revdep/library.noindex/mnem/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas] + #pragma clang diagnostic pop + ^ +17 warnings generated. +clang++ -std=gnu++11 -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 mnem.so RcppExports.o mm.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation +installing to .../revdep/checks.noindex/mnem/old/mnem.Rcheck/00LOCK-mnem/00new/mnem/libs +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘pcalg’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘mnem’ +* removing ‘.../revdep/checks.noindex/mnem/old/mnem.Rcheck/mnem’ + +``` +# MoonlightR + +
+ +* Version: 1.10.0 +* Source code: https://github.com/cran/MoonlightR +* URL: https://github.com/torongs82/Moonlight +* BugReports: https://github.com/torongs82/Moonlight/issues +* Date/Publication: 2019-05-27 +* Number of recursive dependencies: 234 + +Run `revdep_details(,"MoonlightR")` for more info + +
+ +## In both + +* checking whether package ‘MoonlightR’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/MoonlightR/new/MoonlightR.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘MoonlightR’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Warning in fun(libname, pkgname) : couldn't connect to display "" +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘DO.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘MoonlightR’ +* removing ‘.../revdep/checks.noindex/MoonlightR/new/MoonlightR.Rcheck/MoonlightR’ + +``` +### CRAN + +``` +* installing *source* package ‘MoonlightR’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Warning in fun(libname, pkgname) : couldn't connect to display "" +Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : + there is no package called ‘DO.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘MoonlightR’ +* removing ‘.../revdep/checks.noindex/MoonlightR/old/MoonlightR.Rcheck/MoonlightR’ + +``` +# SpaDES.core + +
+ +* Version: 0.2.5 +* Source code: https://github.com/cran/SpaDES.core +* URL: http://spades-core.predictiveecology.org/, https://github.com/PredictiveEcology/SpaDES.core +* BugReports: https://github.com/PredictiveEcology/SpaDES.core/issues +* Date/Publication: 2019-03-19 05:43:37 UTC +* Number of recursive dependencies: 151 + +Run `revdep_details(,"SpaDES.core")` for more info + +
+ +## Newly broken + +* checking installed package size ... NOTE + ``` + installed size is 5.6Mb + sub-directories of 1Mb or more: + R 3.1Mb + doc 1.6Mb + ``` + +## In both + +* checking examples ... ERROR + ``` + ... + + .globals = list(stackName = "landscape", burnStats = "nPixelsBurned") + + ), + + modules = list("caribouMovement"), + + paths = list(modulePath = path) + + ) + Setting: + options( + spades.modulePath = '.../revdep/checks.noindex/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core/sampleModules' + ) + Paths set to: + options( + reproducible.cachePath = '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpvqUB3y/reproducible/cache' + spades.inputPath = '/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpUfXsOm/SpaDES/inputs' + spades.outputPath = '/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpUfXsOm/SpaDES/outputs' + spades.modulePath = '.../revdep/checks.noindex/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core/sampleModules' + ) + Warning in gzfile(file, mode) : + cannot open compressed file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpvqUB3y/reproducible/cache/.Require/_Users_jhester_Dropbox_projects_devtools_revdep_checks.noindex_SpaDES.core_new_SpaDES.core.Rcheck.snapshot.RDS', probable reason 'No such file or directory' + Error in gzfile(file, mode) : cannot open the connection + Calls: simInit ... Require -> installedVersionsQuick -> saveRDS -> gzfile + Execution halted + ``` + +* R CMD check timed out + + +# StarBioTrek + +
+ +* Version: 1.10.0 +* Source code: https://github.com/cran/StarBioTrek +* URL: https://github.com/claudiacava/StarBioTrek +* BugReports: https://github.com/claudiacava/StarBioTrek/issues +* Date/Publication: 2019-05-02 +* Number of recursive dependencies: 236 + +Run `revdep_details(,"StarBioTrek")` for more info + +
+ +## In both + +* checking whether package ‘StarBioTrek’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/StarBioTrek/new/StarBioTrek.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘StarBioTrek’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘miRNAtap.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘StarBioTrek’ +* removing ‘.../revdep/checks.noindex/StarBioTrek/new/StarBioTrek.Rcheck/StarBioTrek’ + +``` +### CRAN + +``` +* installing *source* package ‘StarBioTrek’ ... +** using staged installation +** R +** data +*** moving datasets to lazyload DB +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘miRNAtap.db’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘StarBioTrek’ +* removing ‘.../revdep/checks.noindex/StarBioTrek/old/StarBioTrek.Rcheck/StarBioTrek’ + +``` +# TCGAbiolinks + +
+ +* Version: 2.12.2 +* Source code: https://github.com/cran/TCGAbiolinks +* URL: https://github.com/BioinformaticsFMRP/TCGAbiolinks +* BugReports: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues +* Date/Publication: 2019-06-14 +* Number of recursive dependencies: 252 + +Run `revdep_details(,"TCGAbiolinks")` for more info + +
+ +## In both + +* R CMD check timed out + + +* checking whether package ‘TCGAbiolinks’ can be installed ... WARNING + ``` + Found the following significant warnings: + Warning: objects ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’, ‘.Random.seed’ are created by more than one data call + See ‘.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00install.out’ for details. + ``` + +* checking for missing documentation entries ... WARNING + ``` + Undocumented data sets: + ‘.Random.seed’ + All user-level objects in a package should have documentation entries. + See chapter ‘Writing R documentation files’ in the ‘Writing R + Extensions’ manual. + ``` + +* checking package dependencies ... NOTE + ``` + Package suggested but not available for checking: ‘dnet’ + ``` + +* checking installed package size ... NOTE + ``` + installed size is 97.0Mb + sub-directories of 1Mb or more: + R 2.7Mb + data 4.3Mb + doc 89.8Mb + ``` + +* checking dependencies in R code ... NOTE + ``` + There are ::: calls to the package's namespace in its code. A package + almost never needs to use ::: for its own objects: + ‘move’ + ``` + +* checking R code for possible problems ... NOTE + ``` + ... + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:161-162) + TCGAvisualize_SurvivalCoxNET: no visible global function definition for + ‘dCommSignif’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:174) + TCGAvisualize_SurvivalCoxNET: no visible global function definition for + ‘visNet’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:184-189) + TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:932) + readExonQuantification: no visible binding for global variable ‘exon’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/prepare.R:236-237) + readExonQuantification: no visible binding for global variable + ‘coordinates’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/prepare.R:236-237) + readIDATDNAmethylation: no visible global function definition for + ‘openSesame’ + (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/prepare.R:526) + Undefined global functions or variables: + Tumor.purity barcode c3net clinical coordinates dCommSignif + dNetInduce dNetPipeline exon knnmi.cross limmacontrasts.fit + limmamakeContrasts minet openSesame portions rse_gene value visNet + ``` + +# TCGAbiolinksGUI + +
+ +* Version: 1.10.0 +* Source code: https://github.com/cran/TCGAbiolinksGUI +* Date/Publication: 2019-05-02 +* Number of recursive dependencies: 294 + +Run `revdep_details(,"TCGAbiolinksGUI")` for more info + +
+ +## In both + +* checking whether package ‘TCGAbiolinksGUI’ can be installed ... ERROR + ``` + Installation failed. + See ‘.../revdep/checks.noindex/TCGAbiolinksGUI/new/TCGAbiolinksGUI.Rcheck/00install.out’ for details. + ``` + +## Installation + +### Devel + +``` +* installing *source* package ‘TCGAbiolinksGUI’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ELMER.data’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TCGAbiolinksGUI’ +* removing ‘.../revdep/checks.noindex/TCGAbiolinksGUI/new/TCGAbiolinksGUI.Rcheck/TCGAbiolinksGUI’ + +``` +### CRAN + +``` +* installing *source* package ‘TCGAbiolinksGUI’ ... +** using staged installation +** R +** inst +** byte-compile and prepare package for lazy loading +Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : + there is no package called ‘ELMER.data’ +Calls: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart +Execution halted +ERROR: lazy loading failed for package ‘TCGAbiolinksGUI’ +* removing ‘.../revdep/checks.noindex/TCGAbiolinksGUI/old/TCGAbiolinksGUI.Rcheck/TCGAbiolinksGUI’ + +``` diff --git a/revdep/problems.md b/revdep/problems.md index 90e8faa5d..108014e5a 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,3285 +1,53 @@ -# abjutils +# available -Version: 0.2.1 +
-## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘httr’ ‘progress’ - All declared Imports should be used. - ``` - -# adapr - -Version: 2.0.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘plotly’ ‘shinydashboard’ - All declared Imports should be used. - Missing or unexported object: ‘devtools::clean_source’ - ``` - -# alphavantager - -Version: 0.1.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 2: stop(content, call. = F) at .../revdep/checks.noindex/alphavantager/new/alphavantager.Rcheck/00_pkg_src/alphavantager/R/av_get.R:103 - - ── 3. Error: call Technical Indicators (@test_av_get.R#57) ──────────────────── - Thank you for using Alpha Vantage! Please visit https://www.alphavantage.co/premium/ if you would like to have a higher API call volume.. API parameters used: symbol=MSFT, function=SMA, interval=monthly, time_period=60, series_type=close, apikey=HIDDEN_FOR_YOUR_SAFETY - 1: av_get(symbol, av_fun, interval = interval, time_period = time_period, series_type = series_type) at testthat/test_av_get.R:57 - 2: stop(content, call. = F) at .../revdep/checks.noindex/alphavantager/new/alphavantager.Rcheck/00_pkg_src/alphavantager/R/av_get.R:103 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 7 SKIPPED: 0 FAILED: 3 - 1. Error: call TIMES_SERIES_INTRADAY (@test_av_get.R#22) - 2. Error: call SECTOR (@test_av_get.R#38) - 3. Error: call Technical Indicators (@test_av_get.R#57) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘devtools’ - All declared Imports should be used. - ``` - -# aMNLFA - -Version: 0.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘gridExtra’ - All declared Imports should be used. - ``` - -# amt - -Version: 0.0.5.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rcpp’ ‘magrittr’ - All declared Imports should be used. - ``` - -# annotatr - -Version: 1.6.0 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘annotatr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: build_annotations - > ### Title: A function to build annotations from TxDb.* and AnnotationHub - > ### resources - > ### Aliases: build_annotations - > - > ### ** Examples - > - > # Example with hg19 gene promoters - > annots = c('hg19_genes_promoters') - > annots_gr = build_annotations(genome = 'hg19', annotations = annots) - Error in build_gene_annots(genome = genome, annotations = gene_annotations) : - The package TxDb.Hsapiens.UCSC.hg19.knownGene is not installed, please install it via Bioconductor. - Calls: build_annotations - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - snapshotDate(): 2018-04-30 - Building annotation Gm12878 from AnnotationHub resource AH23256 ... - require("rtracklayer") - downloading 0 resources - loading from cache - '/Users/jhester//.AnnotationHub/28684' - Quitting from lines 153-170 (annotatr-vignette.Rmd) - Error: processing vignette 'annotatr-vignette.Rmd' failed with diagnostics: - The package TxDb.Hsapiens.UCSC.hg19.knownGene is not installed, please install it via Bioconductor. - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - ‘org.Dm.eg.db’ ‘org.Gg.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ - ‘org.Rn.eg.db’ ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’ - ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ - ‘TxDb.Ggallus.UCSC.galGal5.refGene’ - ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ - ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ - ‘TxDb.Mmusculus.UCSC.mm10.knownGene’ - ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’ - ‘TxDb.Rnorvegicus.UCSC.rn5.refGene’ - ‘TxDb.Rnorvegicus.UCSC.rn6.refGene’ - ``` - -* checking R code for possible problems ... NOTE - ``` - plot_coannotations: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/annotatr/new/annotatr.Rcheck/00_pkg_src/annotatr/R/visualize.R:176-178) - plot_numerical_coannotations: no visible binding for global variable - ‘.’ - (.../revdep/checks.noindex/annotatr/new/annotatr.Rcheck/00_pkg_src/annotatr/R/visualize.R:463-480) - plot_numerical_coannotations: no visible binding for global variable - ‘.’ - (.../revdep/checks.noindex/annotatr/new/annotatr.Rcheck/00_pkg_src/annotatr/R/visualize.R:466-471) - plot_numerical_coannotations: no visible binding for global variable - ‘.’ - (.../revdep/checks.noindex/annotatr/new/annotatr.Rcheck/00_pkg_src/annotatr/R/visualize.R:473-478) - Undefined global functions or variables: - . - ``` - -# anomalize - -Version: 0.1.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - help 4.7Mb - ``` - -# anyLib - -Version: 1.0.4 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘curl’ ‘httr’ - All declared Imports should be used. - ``` - -# archivist - -Version: 2.3.1 - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘archivist.github’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘rmarkdown’, ‘archivist.github’ - ``` - -# assertive.code - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Attaching package: 'assertive.base' - - The following objects are masked from 'package:testthat': - - is_false, is_true - - > library(assertive.code) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.code") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.code")) : - could not find function "with_envvar" - Execution halted - ``` - -# assertive.data - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(devtools) - > library(assertive.data) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.data") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.data")) : - could not find function "with_envvar" - Execution halted - ``` - -# assertive.data.uk - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(devtools) - > library(assertive.data.uk) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.data.uk") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.data.uk")) : - could not find function "with_envvar" - Execution halted - ``` - -# assertive.data.us - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(devtools) - > library(assertive.data.us) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.data.us") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.data.us")) : - could not find function "with_envvar" - Execution halted - ``` - -# assertive.matrices - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(devtools) - > library(assertive.matrices) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.matrices") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.matrices")) : - could not find function "with_envvar" - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - ':::' call which should be '::': ‘assertive.base:::print_and_capture’ - See the note in ?`:::` about the use of this operator. - ``` - -# assertive.models - -Version: 0.0-1 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(devtools) - > library(assertive.models) - > - > with_envvar( - + c(LANG = "en_US"), - + test_check("assertive.models") - + ) - Error in with_envvar(c(LANG = "en_US"), test_check("assertive.models")) : - could not find function "with_envvar" - Execution halted - ``` - -# AUCell - -Version: 1.2.4 - -## In both - -* checking package dependencies ... NOTE - ``` - Packages which this enhances but not available for checking: ‘doMC’ ‘doRNG’ - ``` - -* checking dependencies in R code ... NOTE - ``` - 'library' or 'require' call to ‘rbokeh’ in package code. - Please use :: or requireNamespace() instead. - See section 'Suggested packages' in the 'Writing R Extensions' manual. - ``` - -* checking R code for possible problems ... NOTE - ``` - .cellProps_plotTsne: warning in adjustcolor(colorPal(10), alpha = 0.8): - partial argument match of 'alpha' to 'alpha.f' - (.../revdep/checks.noindex/AUCell/new/AUCell.Rcheck/00_pkg_src/AUCell/R/priv_plots.R:127) - AUCell_createViewerApp : : no visible global function - definition for ‘%>%’ - (.../revdep/checks.noindex/AUCell/new/AUCell.Rcheck/00_pkg_src/AUCell/R/aux_createViewerApp.R:224-228) - AUCell_createViewerApp : : no visible binding for global - variable ‘tsne1’ - (.../revdep/checks.noindex/AUCell/new/AUCell.Rcheck/00_pkg_src/AUCell/R/aux_createViewerApp.R:224-228) - AUCell_createViewerApp : : no visible binding for global - variable ‘tsne2’ - (.../revdep/checks.noindex/AUCell/new/AUCell.Rcheck/00_pkg_src/AUCell/R/aux_createViewerApp.R:224-228) - AUCell_createViewerApp : : no visible binding for global - variable ‘cell’ - (.../revdep/checks.noindex/AUCell/new/AUCell.Rcheck/00_pkg_src/AUCell/R/aux_createViewerApp.R:224-228) - Undefined global functions or variables: - %>% cell tsne1 tsne2 - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘SingleCellExperiment’ - ``` - -* checking for unstated dependencies in vignettes ... NOTE - ``` - '::' or ':::' import not declared from: ‘reshape2’ - ``` - -# baytrends - -Version: 1.0.7 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.4Mb - sub-directories of 1Mb or more: - R 2.7Mb - data 1.0Mb - extdata 1.8Mb - ``` - -# BEACH - -Version: 1.2.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘readxl’ - All declared Imports should be used. - ``` - -# beachmat - -Version: 1.2.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 24.8Mb - sub-directories of 1Mb or more: - doc 2.5Mb - lib 16.6Mb - libs 5.2Mb - ``` - -# BETS - -Version: 0.4.4 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘mFilter’ - ``` - -# bigstep - -Version: 1.0.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘methods’ - All declared Imports should be used. - ``` - -# BiocCheck - -Version: 1.16.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Error: processing vignette 'BiocCheck.Rmd' failed with diagnostics: - there is no package called ‘BiocStyle’ - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘codetoolsBioC’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.4Mb - sub-directories of 1Mb or more: - unitTests 4.1Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - ‘knitr:::detect_pattern’ ‘tools:::RdTags’ - See the note in ?`:::` about the use of this operator. - ``` - -# BiocWorkflowTools - -Version: 1.6.2 - -## Newly broken - -* checking examples ... WARNING - ``` - Found the following significant warnings: - - Warning: 'create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Warning: 'use_rstudio' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. - ``` - -## In both - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .travis.yml - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - ‘BiocStyle:::auth_affil_latex’ ‘BiocStyle:::modifyLines’ - ‘rmarkdown:::partition_yaml_front_matter’ - See the note in ?`:::` about the use of this operator. - ``` - -# BioInstaller - -Version: 0.3.6 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - Please input y/n/Y/N! - /var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T//RtmphnLDFa/destdir.initial not empty, overwrite?[y] - More than 3 counts input, default is not to overwrite. - /var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T//RtmphnLDFa/destdir.initial existed, overwrite?[y] - Please input y/n/Y/N! - /var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T//RtmphnLDFa/destdir.initial existed, overwrite?[y] - Please input y/n/Y/N! - /var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T//RtmphnLDFa/destdir.initial existed, overwrite?[y] - More than 3 counts input, default is not to overwrite. - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 62 SKIPPED: 0 FAILED: 1 - 1. Error: install.github (@test_install.R#12) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 10.9Mb - sub-directories of 1Mb or more: - doc 2.5Mb - extdata 8.0Mb - ``` - -# biwavelet - -Version: 0.20.17 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘RColorBrewer’ - ``` - -# BloodCancerMultiOmics2017 - -Version: 1.0.2 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - ... - - The following objects are masked from 'package:IRanges': - - intersect, setdiff, union - - The following objects are masked from 'package:S4Vectors': - - intersect, setdiff, union - - The following objects are masked from 'package:BiocGenerics': - - intersect, setdiff, union - - The following objects are masked from 'package:base': - - intersect, setdiff, union - - Quitting from lines 46-92 (BloodCancerMultiOmics2017.Rmd) - Error: processing vignette 'BloodCancerMultiOmics2017.Rmd' failed with diagnostics: - there is no package called 'org.Hs.eg.db' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘org.Hs.eg.db’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 102.1Mb - sub-directories of 1Mb or more: - data 66.4Mb - doc 26.5Mb - extdata 8.5Mb - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘vsn’ - ``` - -# BrailleR - -Version: 0.29.1 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘installr’ - ``` - -# cartools - -Version: 0.1.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’ - ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’ - All declared Imports should be used. - ``` - -# CGPfunctions - -Version: 0.4 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘devtools’ - All declared Imports should be used. - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘BSDA’, ‘janitor’ - ``` - -# chimeraviz - -Version: 1.6.1 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ - - Depends: includes the non-default packages: - ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Gviz’ ‘S4Vectors’ ‘ensembldb’ - ‘AnnotationFilter’ - Adding so many packages to the search path is excessive and importing - selectively is preferable. - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# chipenrich - -Version: 2.4.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: - ‘org.Dm.eg.db’ ‘org.Dr.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ - ‘org.Rn.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# chipenrich.data - -Version: 2.4.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - ‘GO.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ - ‘org.Rn.eg.db’ ‘TxDb.Dmelanogaster.UCSC.dm3.ensGene’ - ‘TxDb.Dmelanogaster.UCSC.dm6.ensGene’ - ‘TxDb.Drerio.UCSC.danRer10.refGene’ - ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ - ‘TxDb.Mmusculus.UCSC.mm9.knownGene’ - ‘TxDb.Mmusculus.UCSC.mm10.knownGene’ - ‘TxDb.Rnorvegicus.UCSC.rn4.ensGene’ - ‘TxDb.Rnorvegicus.UCSC.rn5.refGene’ - ‘TxDb.Rnorvegicus.UCSC.rn6.refGene’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 153.5Mb - sub-directories of 1Mb or more: - data 152.2Mb - ``` - -# civis - -Version: 1.5.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.4Mb - sub-directories of 1Mb or more: - R 3.1Mb - help 1.7Mb - ``` - -# ClusterJudge - -Version: 1.2.0 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘ClusterJudge-Ex.R’ failed - The error most likely occurred in: - - > ### Name: clusterJudge - > ### Title: judges clustering using an entity.attribute table - > ### Aliases: clusterJudge - > ### Keywords: attribute_mut_inf consolidate_entity_attribute - > - > ### ** Examples - > - > - > library('yeastExpData') - Error in library("yeastExpData") : - there is no package called ‘yeastExpData’ - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Loading ClusterJudge - Loading required package: infotheo - Loading required package: lattice - Loading required package: latticeExtra - Loading required package: RColorBrewer - Loading required package: httr - Loading required package: jsonlite - Warning in readLines(con, warn = FALSE, n = n, ok = ok, skipNul = skipNul) : - invalid input found on input connection '.../revdep/checks.noindex/ClusterJudge/new/ClusterJudge.Rcheck/vign_test/ClusterJudge/R/clusterJudge_z_score.R' - Quitting from lines 61-62 (ClusterJudge-intro.Rmd) - Error: processing vignette 'ClusterJudge-intro.Rmd' failed with diagnostics: - .../revdep/checks.noindex/ClusterJudge/new/ClusterJudge.Rcheck/vign_test/ClusterJudge/R/:24:0: unexpected end of input - 22: ##### z-score definition - 23: ##### z - ^ - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘yeastExpData’ - ``` - -# codemetar - -Version: 0.1.6 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘memoise’ - All declared Imports should be used. - ``` - -# cogena - -Version: 1.14.0 - -## In both - -* checking whether package ‘cogena’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: replacing previous import ‘class::somgrid’ by ‘kohonen::somgrid’ when loading ‘cogena’ - See ‘.../revdep/checks.noindex/cogena/new/cogena.Rcheck/00install.out’ for details. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - doc 1.9Mb - extdata 3.1Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - ‘legend’ - (.../revdep/checks.noindex/cogena/new/cogena.Rcheck/00_pkg_src/cogena/R/heatmapCluster.R:151-153) - heatmapCluster,cogena: no visible global function definition for - ‘legend’ - (.../revdep/checks.noindex/cogena/new/cogena.Rcheck/00_pkg_src/cogena/R/heatmapCluster.R:155-157) - heatmapCluster,cogena: no visible global function definition for - ‘legend’ - (.../revdep/checks.noindex/cogena/new/cogena.Rcheck/00_pkg_src/cogena/R/heatmapCluster.R:159-160) - Undefined global functions or variables: - abline as.dist axis cor data density dist hist image layout legend - lines median mtext order.dendrogram p.adjust par phyper plot.new - rainbow rect reorder sd text title topo.colors - Consider adding - importFrom("grDevices", "rainbow", "topo.colors") - importFrom("graphics", "abline", "axis", "hist", "image", "layout", - "legend", "lines", "mtext", "par", "plot.new", "rect", - "text", "title") - importFrom("stats", "as.dist", "cor", "density", "dist", "median", - "order.dendrogram", "p.adjust", "phyper", "reorder", "sd") - importFrom("utils", "data") - to your NAMESPACE file. - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘clValid’ - ``` - -# COMPASS - -Version: 1.18.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 39-41 (SimpleCOMPASS.Rmd) - Error: processing vignette 'SimpleCOMPASS.Rmd' failed with diagnostics: - there is no package called 'readxl' - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘BiocStyle’ ‘rmarkdown’ - All declared Imports should be used. - ':::' call which should be '::': ‘flowWorkspace:::.getNodeInd’ - See the note in ?`:::` about the use of this operator. - ``` - -* checking R code for possible problems ... NOTE - ``` - COMPASSfitToCountsTable: no visible binding for global variable - ‘population’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:193) - COMPASSfitToCountsTable: no visible binding for global variable ‘Count’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:193) - COMPASSfitToCountsTable: no visible binding for global variable - ‘population’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:194) - COMPASSfitToCountsTable: no visible binding for global variable ‘Count’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:194) - COMPASSfitToCountsTable: no visible binding for global variable ‘id’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:200) - COMPASSfitToCountsTable: no visible binding for global variable ‘id’ - (.../revdep/checks.noindex/COMPASS/new/COMPASS.Rcheck/00_pkg_src/COMPASS/R/utils.R:206) - Undefined global functions or variables: - Count id population - ``` - -* checking for unstated dependencies in vignettes ... NOTE - ``` - 'library' or 'require' calls not declared from: - ‘ggplot2’ ‘readxl’ - ``` - -# CompGLM - -Version: 2.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 122 Variable and function names should be all lowercase. - 123 lines should not be more than 80 characters. - 124 Trailing blank lines are superfluous. - 125 Variable and function names should be all lowercase. - 126 Variable and function names should be all lowercase. - 127 Trailing blank lines are superfluous. - ── 1. Failure: check that package has google style (@test_code_style.R#11) ──── - length(lints) == 0 isn't true. - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 19 SKIPPED: 0 FAILED: 1 - 1. Failure: check that package has google style (@test_code_style.R#11) - - Error: testthat unit tests failed - Execution halted - ``` - -# congressbr - -Version: 0.1.3 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 187 marked UTF-8 strings - ``` - -# CountClust - -Version: 1.8.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.4Mb - sub-directories of 1Mb or more: - data 7.3Mb - ``` - -# crunch - -Version: 1.24.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.4Mb - sub-directories of 1Mb or more: - R 3.5Mb - doc 1.1Mb - ``` - -# curatedMetagenomicData - -Version: 1.10.2 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.7Mb - sub-directories of 1Mb or more: - doc 1.4Mb - help 2.7Mb - ``` - -# demi - -Version: 1.1.2 - -## In both - -* checking R code for possible problems ... NOTE - ``` - ... - diffexp,DEMIDiff: no visible global function definition for ‘p.adjust’ - (.../revdep/checks.noindex/demi/new/demi.Rcheck/00_pkg_src/demi/R/DEMIDiff-methods.R:352) - loadAnnotation,DEMIExperiment-environment: no visible global function - definition for ‘data’ - (.../revdep/checks.noindex/demi/new/demi.Rcheck/00_pkg_src/demi/R/DEMIExperiment-methods.R:549) - loadBlat,DEMIExperiment-environment: no visible global function - definition for ‘data’ - (.../revdep/checks.noindex/demi/new/demi.Rcheck/00_pkg_src/demi/R/DEMIExperiment-methods.R:598) - loadCytoband,DEMIExperiment-environment: no visible global function - definition for ‘data’ - (.../revdep/checks.noindex/demi/new/demi.Rcheck/00_pkg_src/demi/R/DEMIExperiment-methods.R:700) - loadPathway,DEMIExperiment-environment: no visible global function - definition for ‘data’ - (.../revdep/checks.noindex/demi/new/demi.Rcheck/00_pkg_src/demi/R/DEMIExperiment-methods.R:735) - Undefined global functions or variables: - combn data dhyper median p.adjust t.test wilcox.test write.table - Consider adding - importFrom("stats", "dhyper", "median", "p.adjust", "t.test", - "wilcox.test") - importFrom("utils", "combn", "data", "write.table") - to your NAMESPACE file. - ``` - -# derfinder - -Version: 1.14.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE - bptimeout: 2592000; bpprogressbar: FALSE - bplogdir: NA - class: SerialParam - bpisup: TRUE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB - bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE - bptimeout: 2592000; bpprogressbar: FALSE - bplogdir: NA - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 122 SKIPPED: 0 FAILED: 2 - 1. Error: (unknown) (@test_Fstats.R#104) - 2. Error: (unknown) (@test_annotation.R#4) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in citation("BiocStyle") : - no date field in DESCRIPTION file of package 'BiocStyle' - Quitting from lines 63-131 (derfinder-quickstart.Rmd) - Error: processing vignette 'derfinder-quickstart.Rmd' failed with diagnostics: - package 'knitrBootstrap' not found - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.8Mb - sub-directories of 1Mb or more: - doc 5.0Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - ‘GenomeInfoDb:::.guessSpeciesStyle’ - ‘GenomeInfoDb:::.supportedSeqnameMappings’ - See the note in ?`:::` about the use of this operator. - There are ::: calls to the package's namespace in its code. A package - almost never needs to use ::: for its own objects: - ‘.smootherFstats’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ``` - -# derfinderData - -Version: 0.114.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 33.9Mb - sub-directories of 1Mb or more: - extdata 33.7Mb - ``` - -# derfinderHelper - -Version: 1.14.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in citation("BiocStyle") : - no date field in DESCRIPTION file of package 'BiocStyle' - Quitting from lines 61-90 (derfinderHelper.Rmd) - Error: processing vignette 'derfinderHelper.Rmd' failed with diagnostics: - package 'BiocParallel' not found - Execution halted - ``` - -* checking for unstated dependencies in vignettes ... NOTE - ``` - '::' or ':::' import not declared from: ‘RefManageR’ - ``` - -# derfinderPlot - -Version: 1.14.0 - -## In both - -* checking examples ... ERROR - ``` - ... - rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, - union, unique, unsplit, which, which.max, which.min - - - Attaching package: 'S4Vectors' - - The following object is masked from 'package:base': - - expand.grid - - Loading required package: IRanges - Loading required package: GenomeInfoDb - Loading required package: GenomicRanges - Loading required package: foreach - Loading required package: iterators - Loading required package: locfit - locfit 1.5-9.1 2013-03-22 - > library('TxDb.Hsapiens.UCSC.hg19.knownGene') - Error in library("TxDb.Hsapiens.UCSC.hg19.knownGene") : - there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene' - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/test-all.R’ failed. - Last 13 lines of output: - 1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") at testthat/test_adv-plotCluster.R:3 - 2: stop(txt, domain = NA) - - ── 2. Error: (unknown) (@test_plotting.R#14) ────────────────────────────────── - there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene' - 1: library("TxDb.Hsapiens.UCSC.hg19.knownGene") at testthat/test_plotting.R:14 - 2: stop(txt, domain = NA) - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 0 SKIPPED: 0 FAILED: 2 - 1. Error: (unknown) (@test_adv-plotCluster.R#3) - 2. Error: (unknown) (@test_plotting.R#14) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in citation("BiocStyle") : - no date field in DESCRIPTION file of package 'BiocStyle' - Warning in citation("devtools") : - no date field in DESCRIPTION file of package 'devtools' - Quitting from lines 62-115 (derfinderPlot.Rmd) - Error: processing vignette 'derfinderPlot.Rmd' failed with diagnostics: - package 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - ‘org.Hs.eg.db’ ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: 'RefManageR' - All declared Imports should be used. - ``` - -# DLMtool - -Version: 5.2.3 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.7Mb - sub-directories of 1Mb or more: - R 5.2Mb - data 2.1Mb - ``` - -# dodgr - -Version: 0.0.3 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Loading dodgr - Quitting from lines 117-144 (benchmark.Rmd) - Error: processing vignette 'benchmark.Rmd' failed with diagnostics: - polygon edge not found - Execution halted - ``` - -# doRNG - -Version: 1.7.1 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘doMPI’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘doMPI’ - ``` - -# dynutils - -Version: 1.0.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Rcpp’ ‘processx’ - All declared Imports should be used. - ``` - -# elementR - -Version: 1.3.6 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘elementR-Ex.R’ failed - The error most likely occurred in: - - > ### 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 - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - R 2.7Mb - Results 2.3Mb - ``` - -# ELMER.data - -Version: 2.4.2 - -## In both - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .travis.yml - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 288.8Mb - sub-directories of 1Mb or more: - data 286.3Mb - doc 2.4Mb - ``` - -* checking DESCRIPTION meta-information ... NOTE - ``` - Malformed Description field: should contain one or more complete sentences. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Error in .requirePackage(package) : - unable to find required package 'MultiAssayExperiment' - Calls: ... getClass -> getClassDef -> .classEnv -> .requirePackage - Execution halted - ``` - -# epiNEM - -Version: 1.4.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Error: processing vignette 'epiNEM.Rmd' failed with diagnostics: - there is no package called ‘BiocStyle’ - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘org.Sc.sgd.db’ - ``` - -* checking foreign function calls ... NOTE - ``` - Foreign function call to a different package: - .Call("getTruthTable_R", ..., PACKAGE = "BoolNet") - See chapter ‘System and foreign language interfaces’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - plot.epiSim: no visible global function definition for ‘axis’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:375-377) - plot.epiSim: no visible global function definition for ‘boxplot’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:403-405) - plot.epiSim: no visible global function definition for ‘abline’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:407) - plot.epiSim: no visible global function definition for ‘axis’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:409-411) - plot.epiSim: no visible global function definition for ‘boxplot’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:413-415) - plot.epiSim: no visible global function definition for ‘abline’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:417) - plot.epiSim: no visible global function definition for ‘axis’ - (.../revdep/checks.noindex/epiNEM/new/epiNEM.Rcheck/00_pkg_src/epiNEM/R/plot_results.R:419-421) - Undefined global functions or variables: - abline absorption adj axis bnem boxplot computeFc dnf2adj - dummyCNOlist epiNEM2Bg layout popSize preprocessing readSIF sim - simulateStatesRecursive - Consider adding - importFrom("graphics", "abline", "axis", "boxplot", "layout") - to your NAMESPACE file. - ``` - -# EValue - -Version: 1.1.5 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘msm’ - All declared Imports should be used. - ``` - -# excerptr - -Version: 1.4.1 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘excerptr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: excerptr - > ### Title: Excerpt Structuring Comments and Set a Table of Contents. - > ### Aliases: excerptr - > - > ### ** Examples - > - > root <- system.file(package = "excerptr") - > test_files <- file.path(root, "excerpts", "tests", "files") - > excerptr(file_name = file.path(test_files, "some_file.txt"), - + output_path = tempdir(), run_pandoc = FALSE, - + compile_latex = FALSE, - + pandoc_formats = c("tex", "html")) - cloning into '.../inst/excerpts'... - Error in git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, : - Error in 'git2r_clone': unsupported URL protocol - Calls: excerptr -> load_excerpts -> get_excerpts -> - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - "html"), output_path = tempdir(), run_pandoc = TRUE) at testthat/test_basic.R:64 - 2: load_excerpts() at .../revdep/checks.noindex/excerptr/new/excerptr.Rcheck/00_pkg_src/excerptr/R/excerptr.R:36 - 3: get_excerpts(directory = python_directory) at .../revdep/checks.noindex/excerptr/new/excerptr.Rcheck/00_pkg_src/excerptr/R/utils.R:42 - 4: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory) at .../revdep/checks.noindex/excerptr/new/excerptr.Rcheck/00_pkg_src/excerptr/R/get_excerpts.R:21 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 2 SKIPPED: 0 FAILED: 5 - 1. Error: get (@test_basic.R#9) - 2. Error: load (@test_basic.R#15) - 3. Error: md (@test_basic.R#38) - 4. Error: pandoc_formats (@test_basic.R#52) - 5. Error: pandoc_formats_list (@test_basic.R#64) - - Error: testthat unit tests failed - Execution halted - ``` - -# ExPanDaR - -Version: 0.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘CodeDepends’ ‘DT’ ‘PKI’ ‘shinycssloaders’ ‘tictoc’ - All declared Imports should be used. - ``` - -# fakemake - -Version: 1.3.0 - -## Newly broken - -* checking examples ... WARNING - ``` - Found the following significant warnings: - - Warning: 'devtools::create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Warning: 'use_rstudio' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Creating package 'fakepack' in '/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpWyVmqy' - No DESCRIPTION found. Creating with values: - - - Prerequisite DESCRIPTION found. - Prerequisite R/throw.R found. - Prerequisite R/throw.R found. - Prerequisite R/throw.R found. - Prerequisite R/throw.R found. - ``` - -## Newly fixed - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘rcmdcheck’ - ``` - -# fitODBOD - -Version: 1.2.0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘BinaryEPPM’, ‘extraDistr’, ‘triangle’ - ``` - -# gbfs - -Version: 1.0.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 30-31 (kc_bikeshare.Rmd) - Error: processing vignette 'kc_bikeshare.Rmd' failed with diagnostics: - Column `num_bikes_available_types` must be a 1d atomic vector or a list - Execution halted - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘roxygen2’ ‘testthat’ ‘utils’ ‘withr’ - All declared Imports should be used. - ``` - -# ggExtra - -Version: 0.8 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘grDevices’ - All declared Imports should be used. - ``` - -# githubinstall - -Version: 0.2.2 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘mockery’ - All declared Imports should be used. - ``` - -# googleAuthR - -Version: 0.6.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘R6’ - All declared Imports should be used. - ``` - -# gsrc - -Version: 1.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘brassicaData’ - ``` - -# HMP16SData - -Version: 1.0.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - ... - Attaching package: 'dendextend' - - The following object is masked from 'package:stats': - - cutree - - ======================================== - circlize version 0.4.4 - CRAN page: https://cran.r-project.org/package=circlize - Github page: https://github.com/jokergoo/circlize - Documentation: http://jokergoo.github.io/circlize_book/book/ - - If you use it in published research, please cite: - Gu, Z. circlize implements and enhances circular visualization - in R. Bioinformatics 2014. - ======================================== - - Quitting from lines 58-71 (HMP16SData.Rmd) - Error: processing vignette 'HMP16SData.Rmd' failed with diagnostics: - there is no package called 'curatedMetagenomicData' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘curatedMetagenomicData’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 19.1Mb - sub-directories of 1Mb or more: - doc 1.5Mb - extdata 17.4Mb - ``` - -# hyperSpec - -Version: 0.99-20180627 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.3Mb - sub-directories of 1Mb or more: - R 2.0Mb - doc 3.8Mb - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘caTools’ - ``` - -# icd9 - -Version: 1.3.1 - -## Newly broken - -* checking dependencies in R code ... NOTE - ``` - Missing or unexported object: ‘devtools::load_data’ - ``` - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 14 marked Latin-1 strings - Note: found 39 marked UTF-8 strings - ``` - -# IHW - -Version: 1.8.0 - -## 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 42-47 (introduction_to_ihw.Rmd) - Error: processing vignette 'introduction_to_ihw.Rmd' failed with diagnostics: - there is no package called 'airway' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘airway’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 6.2Mb - sub-directories of 1Mb or more: - doc 5.8Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/plots.R:101) - plot_decisionboundary: no visible binding for global variable - ‘covariate’ - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/plots.R:110-112) - plot_decisionboundary: no visible binding for global variable ‘pvalue’ - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/plots.R:110-112) - plot_decisionboundary: no visible binding for global variable ‘fold’ - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/plots.R:110-112) - thresholds_ihwResult: no visible global function definition for - ‘na.exclude’ - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/ihw_class.R:96-97) - thresholds,ihwResult: no visible global function definition for - ‘na.exclude’ - (.../revdep/checks.noindex/IHW/new/IHW.Rcheck/00_pkg_src/IHW/R/ihw_class.R:96-97) - Undefined global functions or variables: - covariate fold gurobi mcols mcols<- metadata metadata<- na.exclude - p.adjust pvalue runif str stratum - Consider adding - importFrom("stats", "na.exclude", "p.adjust", "runif") - importFrom("utils", "str") - to your NAMESPACE file. - ``` - -# iLaplace - -Version: 1.1.0 - -## In both - -* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... WARNING - ``` - apparently using $(LAPACK_LIBS) without following $(BLAS_LIBS) in ‘src/Makevars’ - ``` - -# KoNLP - -Version: 0.80.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.6Mb - sub-directories of 1Mb or more: - java 6.0Mb - ``` - -# likert - -Version: 1.3.5 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 7 marked UTF-8 strings - ``` - -# lilikoi - -Version: 0.1.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.2Mb - sub-directories of 1Mb or more: - data 3.8Mb - extdata 1.1Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 3837 marked UTF-8 strings - ``` - -# lime - -Version: 0.4.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: - ‘glmnet’ ‘ggplot2’ ‘stringi’ ‘stringdist’ ‘htmlwidgets’ ‘shiny’ - ‘shinythemes’ ‘magick’ ‘gower’ ‘RcppEigen’ - - Packages suggested but not available for checking: - ‘xgboost’ ‘testthat’ ‘mlr’ ‘h2o’ ‘text2vec’ ‘knitr’ ‘rmarkdown’ - ‘keras’ - - VignetteBuilder package required for checking but not installed: ‘knitr’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# loose.rock - -Version: 1.0.9 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘futile.options’ ‘ggfortify’ ‘grDevices’ ‘stats’ - All declared Imports should be used. - ``` - -# Luminescence - -Version: 0.8.5 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.7Mb - sub-directories of 1Mb or more: - R 6.2Mb - ``` - -# MCbiclust - -Version: 1.4.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘GO.db’ ‘org.Hs.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# metafolio - -Version: 0.1.0 - -## In both - -* checking R code for possible problems ... NOTE - ``` - ... - plot_sp_A_ts: no visible global function definition for ‘axis’ - (.../revdep/checks.noindex/metafolio/new/metafolio.Rcheck/00_pkg_src/metafolio/R/plot_sp_A_ts.R:90-91) - run_cons_plans: no visible binding for global variable ‘var’ - thermal_area: no visible global function definition for ‘uniroot’ - (.../revdep/checks.noindex/metafolio/new/metafolio.Rcheck/00_pkg_src/metafolio/R/thermal_integration.R:19-21) - thermal_area: no visible global function definition for ‘uniroot’ - (.../revdep/checks.noindex/metafolio/new/metafolio.Rcheck/00_pkg_src/metafolio/R/thermal_integration.R:22-24) - thermal_area: no visible global function definition for ‘integrate’ - (.../revdep/checks.noindex/metafolio/new/metafolio.Rcheck/00_pkg_src/metafolio/R/thermal_integration.R:26-28) - Undefined global functions or variables: - abline axTicks axis barplot box chull contourLines hcl integrate - legend lines lm matplot mtext na.omit optimize par plot plot.default - points polygon quantile rect rnorm runif text uniroot var - Consider adding - importFrom("grDevices", "chull", "contourLines", "hcl") - importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box", - "legend", "lines", "matplot", "mtext", "par", "plot", - "plot.default", "points", "polygon", "rect", "text") - importFrom("stats", "integrate", "lm", "na.omit", "optimize", - "quantile", "rnorm", "runif", "uniroot", "var") - to your NAMESPACE file. - ``` - -# metagenomeFeatures - -Version: 2.0.0 - -## In both - -* checking whether package ‘metagenomeFeatures’ can be installed ... WARNING - ``` - Found the following significant warnings: - Warning: subclass "QualityScaledDNAStringSet" of class "DNAStringSet" is not local and cannot be updated for new inheritance information; consider setClassUnion() - Warning: replacing previous import ‘lazyeval::is_formula’ by ‘purrr::is_formula’ when loading ‘metagenomeFeatures’ - Warning: replacing previous import ‘lazyeval::is_atomic’ by ‘purrr::is_atomic’ when loading ‘metagenomeFeatures’ - See ‘.../revdep/checks.noindex/metagenomeFeatures/new/metagenomeFeatures.Rcheck/00install.out’ for details. - ``` - -* checking for missing documentation entries ... WARNING - ``` - Undocumented S4 methods: - generic '[' and siglist 'mgFeatures' - All user-level objects in a package (including S4 classes and methods) - should have documentation entries. - See chapter ‘Writing R documentation files’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - extdata 3.5Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - .select: no visible binding for global variable ‘identifier’ - (.../revdep/checks.noindex/metagenomeFeatures/new/metagenomeFeatures.Rcheck/00_pkg_src/metagenomeFeatures/R/mgDb_method_select.R:96-97) - .select.taxa: no visible binding for global variable ‘Keys’ - (.../revdep/checks.noindex/metagenomeFeatures/new/metagenomeFeatures.Rcheck/00_pkg_src/metagenomeFeatures/R/mgDb_method_select.R:21) - .select.taxa: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/metagenomeFeatures/new/metagenomeFeatures.Rcheck/00_pkg_src/metagenomeFeatures/R/mgDb_method_select.R:21) - get_gg13.8_85MgDb: no visible binding for global variable ‘metadata’ - (.../revdep/checks.noindex/metagenomeFeatures/new/metagenomeFeatures.Rcheck/00_pkg_src/metagenomeFeatures/R/gg13.8_85MgDb.R:23-25) - Undefined global functions or variables: - . Keys identifier metadata - ``` - -# micompr - -Version: 1.1.0 - -## In both - -* checking examples ... ERROR - ``` - ... - Running examples in ‘micompr-Ex.R’ failed - The error most likely occurred in: - - > ### Name: assumptions.cmpoutput - > ### Title: Get assumptions for parametric tests performed on output - > ### comparisons - > ### Aliases: assumptions.cmpoutput - > - > ### ** Examples - > - > - > # Create a cmpoutput object from the provided datasets - > cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls) - > - > # Get the assumptions for the parametric tests performed in cmp - > acmp <- assumptions(cmp) - sROC 0.1-2 loaded - MANOVA assumptions require 'MVN' and 'biotools' packages. - Error in `*tmp*`[[i]] : subscript out of bounds - Calls: assumptions -> assumptions.cmpoutput - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - subscript out of bounds - 1: assumptions(mic1a) at testthat/test_micomp.R:281 - 2: assumptions.micomp(mic1a) at .../revdep/checks.noindex/micompr/new/micompr.Rcheck/00_pkg_src/micompr/R/assumptions.R:19 - 3: lapply(obj, function(x) assumptions(x)) at .../revdep/checks.noindex/micompr/new/micompr.Rcheck/00_pkg_src/micompr/R/micomp.R:498 - 4: FUN(X[[i]], ...) - 5: assumptions(x) at .../revdep/checks.noindex/micompr/new/micompr.Rcheck/00_pkg_src/micompr/R/micomp.R:498 - 6: assumptions.cmpoutput(x) at .../revdep/checks.noindex/micompr/new/micompr.Rcheck/00_pkg_src/micompr/R/assumptions.R:19 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 363 SKIPPED: 0 FAILED: 2 - 1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) - 2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) - - Error: testthat unit tests failed - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 341-342 (paper.Rnw) - Error: processing vignette 'paper.Rnw' failed with diagnostics: - subscript out of bounds - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘biotools’ - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘biotools’ - ``` - -# microsamplingDesign - -Version: 1.0.5 - -## Newly broken - -* checking whether package ‘microsamplingDesign’ can be installed ... ERROR - ``` - Installation failed. - See ‘.../revdep/checks.noindex/microsamplingDesign/new/microsamplingDesign.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘microsamplingDesign’ ... -** package ‘microsamplingDesign’ successfully unpacked and MD5 sums checked -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/microsamplingDesign/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/microsamplingDesign/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c interpolation.cpp -o interpolation.o -clang++ -std=gnu++11 -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 microsamplingDesign.so RcppExports.o interpolation.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -installing to .../revdep/checks.noindex/microsamplingDesign/new/microsamplingDesign.Rcheck/microsamplingDesign/libs -** R -** inst -** byte-compile and prepare package for lazy loading -Error : object ‘dev_package_deps’ is not exported by 'namespace:devtools' -ERROR: lazy loading failed for package ‘microsamplingDesign’ -* removing ‘.../revdep/checks.noindex/microsamplingDesign/new/microsamplingDesign.Rcheck/microsamplingDesign’ - -``` -### CRAN - -``` -* installing *source* package ‘microsamplingDesign’ ... -** package ‘microsamplingDesign’ successfully unpacked and MD5 sums checked -** libs -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/microsamplingDesign/Rcpp/include" -I".../revdep/library.noindex/microsamplingDesign/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o -clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/microsamplingDesign/Rcpp/include" -I".../revdep/library.noindex/microsamplingDesign/RcppArmadillo/include" -I/usr/local/include -fPIC -Wall -g -O2 -c interpolation.cpp -o interpolation.o -clang++ -std=gnu++11 -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 microsamplingDesign.so RcppExports.o interpolation.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0' -ld: warning: directory not found for option '-L/usr/local/gfortran/lib' -installing to .../revdep/checks.noindex/microsamplingDesign/old/microsamplingDesign.Rcheck/microsamplingDesign/libs -** R -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded -* DONE (microsamplingDesign) - -``` -# MODIS - -Version: 1.1.3 - -## In both - -* checking S3 generic/method consistency ... WARNING - ``` - sh: gdalinfo: command not found - See section ‘Generic functions and methods’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking replacement functions ... WARNING - ``` - sh: gdalinfo: command not found - The argument of a replacement function which corresponds to the right - hand side must be named ‘value’. - ``` - -* checking for missing documentation entries ... WARNING - ``` - sh: gdalinfo: command not found - All user-level objects in a package should have documentation entries. - See chapter ‘Writing R documentation files’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking for code/documentation mismatches ... WARNING - ``` - sh: gdalinfo: command not found - sh: gdalinfo: command not found - sh: gdalinfo: command not found - ``` - -* checking dependencies in R code ... NOTE - ``` - sh: gdalinfo: command not found - ``` - -* checking foreign function calls ... NOTE - ``` - sh: gdalinfo: command not found - See chapter ‘System and foreign language interfaces’ in the ‘Writing R - Extensions’ manual. - ``` - -* checking Rd \usage sections ... NOTE - ``` - sh: gdalinfo: command not found - The \usage entries for S3 methods should use the \method markup and not - their full name. - See chapter ‘Writing R documentation files’ in the ‘Writing R - Extensions’ manual. - ``` - -# MonetDBLite - -Version: 0.6.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.0Mb - sub-directories of 1Mb or more: - libs 5.3Mb - ``` - -# MoonlightR - -Version: 1.6.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 11.3Mb - sub-directories of 1Mb or more: - data 3.1Mb - doc 7.9Mb - ``` - -# msgtools - -Version: 0.2.7 - -## Newly broken - -* checking examples ... WARNING - ``` - Found the following significant warnings: - - Warning: 'create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Warning: 'create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Warning: 'create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Warning: 'create' is deprecated. - Warning: 'setup' is deprecated. - Warning: 'create_description' is deprecated. - Deprecated functions may be defunct as soon as of the next release of - R. - See ?Deprecated. - ``` - -# myTAI - -Version: 0.8.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - data 2.0Mb - doc 2.4Mb - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘biomartr’ - All declared Imports should be used. - ``` - -# networktools - -Version: 1.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘devtools’ - All declared Imports should be used. - ``` - -# nima - -Version: 0.5.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’ - All declared Imports should be used. - ``` - -# NlsyLinks - -Version: 2.0.6 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 8.7Mb - sub-directories of 1Mb or more: - data 4.3Mb - reports 2.2Mb - ``` - -# NMF - -Version: 0.21.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘doMPI’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.3Mb - sub-directories of 1Mb or more: - R 3.2Mb - ``` - -# npsm - -Version: 0.5 - -## In both - -* checking R code for possible problems ... NOTE - ``` - ... - onecovahomog: no visible global function definition for ‘pf’ - (.../revdep/checks.noindex/npsm/new/npsm.Rcheck/00_pkg_src/npsm/R/racov.r:53) - rank.test: no visible global function definition for ‘pnorm’ - (.../revdep/checks.noindex/npsm/new/npsm.Rcheck/00_pkg_src/npsm/R/rank.test.r:12-16) - rank.test: no visible global function definition for ‘coef’ - (.../revdep/checks.noindex/npsm/new/npsm.Rcheck/00_pkg_src/npsm/R/rank.test.r:21) - rank.test: no visible global function definition for ‘qt’ - (.../revdep/checks.noindex/npsm/new/npsm.Rcheck/00_pkg_src/npsm/R/rank.test.r:24-28) - rcn: no visible global function definition for ‘rnorm’ - vanElteren.test: no visible global function definition for ‘pnorm’ - (.../revdep/checks.noindex/npsm/new/npsm.Rcheck/00_pkg_src/npsm/R/vanElteren.test.r:23) - Undefined global functions or variables: - coef cor dnorm median model.matrix new pchisq pf pnorm qnorm qt - quantile resid rnorm var - Consider adding - importFrom("methods", "new") - importFrom("stats", "coef", "cor", "dnorm", "median", "model.matrix", - "pchisq", "pf", "pnorm", "qnorm", "qt", "quantile", "resid", - "rnorm", "var") - to your NAMESPACE file (and ensure that your DESCRIPTION Imports field - contains 'methods'). - ``` - -# opencpu - -Version: 2.0.8 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 4 marked UTF-8 strings - ``` - -# OpenMx - -Version: 2.11.3 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘Rmpi’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 18.2Mb - sub-directories of 1Mb or more: - R 6.6Mb - libs 4.1Mb - models 4.7Mb - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘ifaTools’, ‘umx’ - ``` - -# openPrimeR - -Version: 1.2.0 - -## In both - -* checking for hidden files and directories ... NOTE - ``` - Found the following hidden files and directories: - .travis.yml - These were most likely included in error. See section ‘Package - structure’ in the ‘Writing R Extensions’ manual. - ``` - -* checking installed package size ... NOTE - ``` - installed size is 15.2Mb - sub-directories of 1Mb or more: - R 3.9Mb - extdata 10.2Mb - ``` - -# OPWeight - -Version: 1.2.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - ... - ... - Installing package into '.../revdep/checks.noindex/OPWeight/new/OPWeight.Rcheck' - (as 'lib' is unspecified) - trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/BiocInstaller_1.30.0.tgz' - Content type 'application/x-gzip' length 84646 bytes (82 KB) - ================================================== - downloaded 82 KB - - Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help - BioC_mirror: https://bioconductor.org - Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). - Installing package(s) 'OPWeight' - trying URL 'https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/OPWeight_1.2.0.tgz' - Content type 'application/x-gzip' length 632632 bytes (617 KB) - ================================================== - downloaded 617 KB - - Quitting from lines 46-59 (OPWeight.Rmd) - Error: processing vignette 'OPWeight.Rmd' failed with diagnostics: - there is no package called 'airway' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘airway’ - ``` - -# osmplotr - -Version: 0.3.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.9Mb - sub-directories of 1Mb or more: - doc 5.9Mb - ``` - -# packrat - -Version: 0.4.9-3 - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘BiocInstaller’ - ``` - -# pacman - -Version: 0.4.6 - -## Newly broken - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - 9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpROUfuj/R.INSTALL1463c63119464/remotes/R/install-remote.R:73 - 10: FUN(X[[i]], ...) - 11: remote_package_name(remote) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpROUfuj/R.INSTALL1463c63119464/remotes/R/install-remote.R:24 - 12: remote_package_name.github_remote(remote) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpROUfuj/R.INSTALL1463c63119464/remotes/R/install-remote.R:105 - 13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, - host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), - use_curl = use_curl) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpROUfuj/R.INSTALL1463c63119464/remotes/R/install-github.R:222 - 14: stop("HTTP error ", res$status_code, ".", "\n", github_error_message(res), call. = FALSE) at /private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpROUfuj/R.INSTALL1463c63119464/remotes/R/github.R:101 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 54 SKIPPED: 3 FAILED: 1 - 1. Error: p_install_gh works (@test-p_install_gh.R#5) - - Error: testthat unit tests failed - Execution halted - ``` - -# parlitools - -Version: 0.2.1 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 13 marked UTF-8 strings - ``` - -# pkgdown - -Version: 1.1.0 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - nrow(out) not equal to 1. - 1/1 mismatches - [1] 0 - 1 == -1 - - ── 2. Failure: can autodetect published tutorials (@test-tutorials.R#31) ────── - out$name not equal to "test-1". - Lengths differ: 0 is not 1 - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 241 SKIPPED: 9 FAILED: 2 - 1. Failure: can autodetect published tutorials (@test-tutorials.R#30) - 2. Failure: can autodetect published tutorials (@test-tutorials.R#31) - - Error: testthat unit tests failed - Execution halted - ``` - -# pkgmaker - -Version: 0.27 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘magrittr’ ‘stringi’ - All declared Imports should be used. - ``` - -# pkgnet - -Version: 0.2.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘DT’ ‘covr’ ‘knitr’ - All declared Imports should be used. - ``` - -# PKPDmisc - -Version: 2.1.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘purrr’ - All declared Imports should be used. - ``` - -# plotly - -Version: 4.8.0 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 6.5Mb - sub-directories of 1Mb or more: - R 1.7Mb - htmlwidgets 3.1Mb - ``` - -# poio - -Version: 0.0-3 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘ISOcodes’ - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 8 marked UTF-8 strings - ``` - -# prodigenr - -Version: 0.4.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘clipr’ ‘desc’ ‘devtools’ - All declared Imports should be used. - ``` - -# PSAboot - -Version: 1.1.4 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 4 marked UTF-8 strings - ``` - -# psichomics - -Version: 1.6.1 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 9.6Mb - sub-directories of 1Mb or more: - R 2.9Mb - doc 5.6Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:284) - prepareGeneQuantSTAR : : no visible binding for global - variable ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:284) - prepareGeneQuantSTAR : : no visible binding for global - variable ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:285) - prepareJunctionQuantSTAR: no visible binding for '<<-' assignment to - ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:198) - prepareJunctionQuantSTAR : : no visible binding for '<<-' - assignment to ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:200) - prepareJunctionQuantSTAR : : no visible binding for global - variable ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:200) - prepareJunctionQuantSTAR : : no visible binding for global - variable ‘index’ - (.../revdep/checks.noindex/psichomics/new/psichomics.Rcheck/00_pkg_src/psichomics/R/data_local.R:201) - Undefined global functions or variables: - ..strandedness index - ``` - -* checking compiled code ... NOTE - ``` - File ‘psichomics/libs/psichomics.so’: - Found ‘___stdoutp’, possibly from ‘stdout’ (C) - Object: ‘psiFastCalc.o’ - Found ‘_printf’, possibly from ‘printf’ (C) - Object: ‘psiFastCalc.o’ - Found ‘_putchar’, possibly from ‘putchar’ (C) - Object: ‘psiFastCalc.o’ - - Compiled code should not call entry points which might terminate R nor - write to stdout/stderr instead of to the console, nor use Fortran I/O - nor system RNGs. - - See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. - ``` - -# PSPManalysis - -Version: 0.2.0 - -## Newly broken - -* checking whether package ‘PSPManalysis’ can be installed ... ERROR - ``` - Installation failed. - See ‘.../revdep/checks.noindex/PSPManalysis/new/PSPManalysis.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘PSPManalysis’ ... -** package ‘PSPManalysis’ successfully unpacked and MD5 sums checked -** libs -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c PSPManalysis_init.c -o PSPManalysis_init.o -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c csb2rlist.c -o csb2rlist.o -clang -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 PSPManalysis.so PSPManalysis_init.o csb2rlist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to .../revdep/checks.noindex/PSPManalysis/new/PSPManalysis.Rcheck/PSPManalysis/libs -** R -** demo -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded -Error: package or namespace load failed for ‘PSPManalysis’: - .onAttach failed in attachNamespace() for 'PSPManalysis', details: - call: NULL - error: 'setup_rtools' is not an exported object from 'namespace:devtools' -Error: loading failed -Execution halted -ERROR: loading failed -* removing ‘.../revdep/checks.noindex/PSPManalysis/new/PSPManalysis.Rcheck/PSPManalysis’ - -``` -### CRAN - -``` -* installing *source* package ‘PSPManalysis’ ... -** package ‘PSPManalysis’ successfully unpacked and MD5 sums checked -** libs -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c PSPManalysis_init.c -o PSPManalysis_init.o -clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c csb2rlist.c -o csb2rlist.o -clang -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 PSPManalysis.so PSPManalysis_init.o csb2rlist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation -installing to .../revdep/checks.noindex/PSPManalysis/old/PSPManalysis.Rcheck/PSPManalysis/libs -** R -** demo -** inst -** byte-compile and prepare package for lazy loading -** help -*** installing help indices -** building package indices -** installing vignettes -** testing if installed package can be loaded -* DONE (PSPManalysis) - -``` -# pulver - -Version: 0.1.0 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘DatABEL’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# qqplotr - -Version: 0.0.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘knitr’ ‘purrr’ ‘rmarkdown’ - All declared Imports should be used. - ``` - -# qsort - -Version: 0.2.2 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 6 marked UTF-8 strings - ``` - -# rbundler - -Version: 0.3.7 - -## In both - -* checking DESCRIPTION meta-information ... NOTE - ``` - Malformed Title field: should not end in a period. - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - install_version: no visible global function definition for - ‘contrib.url’ - (.../revdep/checks.noindex/rbundler/new/rbundler.Rcheck/00_pkg_src/rbundler/R/install_version.r:25) - install_version: no visible global function definition for - ‘available.packages’ - (.../revdep/checks.noindex/rbundler/new/rbundler.Rcheck/00_pkg_src/rbundler/R/install_version.r:26) - install_version: no visible global function definition for - ‘install_url’ - (.../revdep/checks.noindex/rbundler/new/rbundler.Rcheck/00_pkg_src/rbundler/R/install_version.r:37) - load_available_packages: no visible global function definition for - ‘contrib.url’ - (.../revdep/checks.noindex/rbundler/new/rbundler.Rcheck/00_pkg_src/rbundler/R/load_available_packages.r:5) - validate_installed_package: no visible global function definition for - ‘installed.packages’ - (.../revdep/checks.noindex/rbundler/new/rbundler.Rcheck/00_pkg_src/rbundler/R/install_version.r:55) - Undefined global functions or variables: - available.packages contrib.url install_url installed.packages - Consider adding - importFrom("utils", "available.packages", "contrib.url", - "installed.packages") - to your NAMESPACE file. - ``` - -# RcppProgress - -Version: 0.4.1 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - - ── 4. Failure: eta_progress_bar (@test-pkg_examples.R#28) ───────────────────── - `eta_progress_bar(nb = 1000)` threw an error. - Message: System command error - Class: system_command_status_error/system_command_error/error/condition - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 0 SKIPPED: 0 FAILED: 4 - 1. Failure: test_sequential (@test-pkg_examples.R#6) - 2. Failure: test_multithreaded (@test-pkg_examples.R#13) - 3. Failure: amardillo_multithreaded (@test-pkg_examples.R#20) - 4. Failure: eta_progress_bar (@test-pkg_examples.R#28) - - Error: testthat unit tests failed - Execution halted - ``` - -# recount - -Version: 1.6.3 - -## In both - -* R CMD check timed out - - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘EnsDb.Hsapiens.v79’ - ``` - -* checking installed package size ... NOTE - ``` - installed size is 15.7Mb - sub-directories of 1Mb or more: - data 12.1Mb - doc 3.3Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 347 marked UTF-8 strings - ``` - -# regionReport - -Version: 1.14.3 - -## In both - -* checking examples ... ERROR - ``` - ... - ordinary text without R code - - label: reproducibility1 (with options) - List of 1 - $ echo: logi FALSE - - ordinary text without R code - - label: reproducibility2 (with options) - List of 1 - $ echo: logi FALSE - - ordinary text without R code - - label: reproducibility3 (with options) - List of 1 - $ echo: logi FALSE - - Quitting from lines 341-344 (DESeq2Exploration.Rmd) - Error: 'sessioninfo' >= * must be installed for this functionality. - Execution halted - ``` - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 126-135 (bumphunterExample.Rmd) - Error: processing vignette 'bumphunterExample.Rmd' failed with diagnostics: - 'sessioninfo' >= * must be installed for this functionality. - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Unexported object imported by a ':::' call: ‘DESeq2:::pvalueAdjustment’ - See the note in ?`:::` about the use of this operator. - ``` - -# reprex - -Version: 0.2.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘tools’ - All declared Imports should be used. - ``` - -# reproducible - -Version: 0.2.3 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘gdalUtils’ - All declared Imports should be used. - ``` - -# rfishbase - -Version: 2.1.2 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 44 marked UTF-8 strings - ``` - -# Ricetl - -Version: 0.2.5 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘gWidgetsRGtk2’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` - -# RIVER - -Version: 1.4.0 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘data.table’ - ``` - -# rnaturalearth - -Version: 0.1.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rnaturalearthhires’ - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 7 marked Latin-1 strings - ``` - -# rpivotTable - -Version: 0.3.0 - -## In both - -* checking package dependencies ... NOTE - ``` - Package which this enhances but not available for checking: ‘shiny’ - ``` - -# rsimsum - -Version: 0.3.3 - -## In both - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘ggthemes’ - ``` - -# rsMove - -Version: 0.2.4 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘gdalUtils’ ‘igraph’ ‘lattice’ ‘lubridate’ ‘randomForest’ ‘rgdal’ - ‘spatialEco’ - All declared Imports should be used. - ``` - -# rsoi - -Version: 0.3.0 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘utils’ - All declared Imports should be used. - ``` - -# RTCGA - -Version: 1.10.0 - -## In both - -* checking examples ... ERROR - ``` - Running examples in ‘RTCGA-Ex.R’ failed - The error most likely occurred in: - - > ### Name: boxplotTCGA - > ### Title: Create Boxplots for TCGA Datasets - > ### Aliases: boxplotTCGA - > - > ### ** Examples - > - > library(RTCGA.rnaseq) - Error in library(RTCGA.rnaseq) : - there is no package called ‘RTCGA.rnaseq’ - Execution halted - ``` - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Complete output: - > library(testthat) - > library(RTCGA) - Welcome to the RTCGA (version: 1.10.0). - > library(RTCGA.rnaseq) - Error in library(RTCGA.rnaseq) : - there is no package called 'RTCGA.rnaseq' - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Packages suggested but not available for checking: - ‘RTCGA.rnaseq’ ‘RTCGA.clinical’ ‘RTCGA.mutations’ ‘RTCGA.RPPA’ - ‘RTCGA.mRNA’ ‘RTCGA.miRNASeq’ ‘RTCGA.methylation’ ‘RTCGA.CNV’ - ‘RTCGA.PANCAN12’ - ``` - -* checking R code for possible problems ... NOTE - ``` - ... - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) - ggbiplot: no visible binding for global variable ‘xvar’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) - ggbiplot: no visible binding for global variable ‘yvar’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) - ggbiplot: no visible binding for global variable ‘angle’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) - ggbiplot: no visible binding for global variable ‘hjust’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/ggbiplot.R:157-161) - read.mutations: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:383) - read.mutations: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:386) - read.rnaseq: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/readTCGA.R:372-375) - survivalTCGA: no visible binding for global variable ‘times’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/survivalTCGA.R:101-137) - whichDateToUse: no visible binding for global variable ‘.’ - (.../revdep/checks.noindex/RTCGA/new/RTCGA.Rcheck/00_pkg_src/RTCGA/R/downloadTCGA.R:167-168) - Undefined global functions or variables: - . angle hjust muted times varname xvar yvar - ``` - -* checking Rd cross-references ... NOTE - ``` - Packages unavailable to check Rd xrefs: ‘RTCGA.rnaseq’, ‘RTCGA.clinical’, ‘RTCGA.mutations’, ‘RTCGA.CNV’, ‘RTCGA.RPPA’, ‘RTCGA.mRNA’, ‘RTCGA.miRNASeq’, ‘RTCGA.methylation’ - ``` +* Version: 1.0.2 +* Source code: https://github.com/cran/available +* URL: https://github.com/ropenscilabs/available +* BugReports: https://github.com/ropenscilabs/available/issues +* Date/Publication: 2018-11-08 15:40:18 UTC +* Number of recursive dependencies: 73 -# RtutoR +Run `revdep_details(,"available")` for more info -Version: 1.2 +
-## In both +## Newly broken * checking dependencies in R code ... NOTE ``` - Namespaces in Imports field not imported from: - ‘DT’ ‘rmarkdown’ - All declared Imports should be used. - ``` - -# Ryacas - -Version: 0.3-1 - -## In both - -* checking whether package ‘Ryacas’ can be installed ... WARNING - ``` - Found the following significant warnings: - yacas/src/obmalloc.cpp:584:23: warning: comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare] - See ‘.../revdep/checks.noindex/Ryacas/new/Ryacas.Rcheck/00install.out’ for details. - ``` - -# SciencesPo - -Version: 1.4.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Warning in engine$weave(file, quiet = quiet, encoding = enc) : - The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it. - SciencesPo 1.4.1 - Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead - Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing - Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead - Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing - Quitting from lines 754-756 (Indices.Rmd) - Error: processing vignette 'Indices.Rmd' failed with diagnostics: - 'sessioninfo' >= * must be installed for this functionality. - Execution halted - ``` - -* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘gmodels’ - ``` - -# segclust2d - -Version: 0.1.0 - -## In both - -* checking whether package ‘segclust2d’ can be installed ... ERROR - ``` - Installation failed. - See ‘.../revdep/checks.noindex/segclust2d/new/segclust2d.Rcheck/00install.out’ for details. - ``` - -## Installation - -### Devel - -``` -* installing *source* package ‘segclust2d’ ... -** package ‘segclust2d’ successfully unpacked and MD5 sums checked -** libs -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c RcppExports.cpp -o RcppExports.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_DynProg.cpp -o SegTraj_DynProg.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_EM.cpp -o SegTraj_EM.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/devtools/new/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_Gmixt.cpp -o SegTraj_Gmixt.o -clang: clang: error: unsupported option '-fopenmp'error -: unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -make: *** [SegTraj_EM.o] Error 1 -make: *** Waiting for unfinished jobs.... -make: *** [SegTraj_DynProg.o] Error 1 -make: *** [RcppExports.o] Error 1 -make: *** [SegTraj_Gmixt.o] Error 1 -ERROR: compilation failed for package ‘segclust2d’ -* removing ‘.../revdep/checks.noindex/segclust2d/new/segclust2d.Rcheck/segclust2d’ - -``` -### CRAN - -``` -* installing *source* package ‘segclust2d’ ... -** package ‘segclust2d’ successfully unpacked and MD5 sums checked -** libs -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/segclust2d/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c RcppExports.cpp -o RcppExports.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/segclust2d/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_DynProg.cpp -o SegTraj_DynProg.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/segclust2d/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_EM.cpp -o SegTraj_EM.o -clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I".../revdep/library.noindex/segclust2d/Rcpp/include" -I".../revdep/library.noindex/segclust2d/RcppArmadillo/include" -I/usr/local/include -fopenmp -fPIC -Og -g -Wextra -Wno-unused-parameter -Wpedantic -fcolor-diagnostics -c SegTraj_Gmixt.cpp -o SegTraj_Gmixt.o -clang: clang: errorclang: : unsupported option '-fopenmp'error: unsupported option '-fopenmp'error: - -unsupported option '-fopenmp' -clang: error: unsupported option '-fopenmp' -make: *** [SegTraj_EM.o] Error 1 -make: *** Waiting for unfinished jobs.... -make: *** [SegTraj_Gmixt.o] Error 1 -make: *** [SegTraj_DynProg.o] Error 1 -make: *** [RcppExports.o] Error 1 -ERROR: compilation failed for package ‘segclust2d’ -* removing ‘.../revdep/checks.noindex/segclust2d/old/segclust2d.Rcheck/segclust2d’ - -``` -# soilcarbon - -Version: 1.2.0 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 145 marked UTF-8 strings - ``` - -# SpaDES - -Version: 2.0.2 - -## In both - -* checking package dependencies ... ERROR - ``` - Package required but not available: ‘SpaDES.core’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Missing or unexported object: ‘devtools::create’ ``` -# SpaDES.addins - -Version: 0.1.1 - ## In both -* checking package dependencies ... ERROR +* checking package dependencies ... NOTE ``` - Package required but not available: ‘SpaDES.core’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Package suggested but not available for checking: ‘BiocInstaller’ ``` -# specmine - -Version: 2.0.3 +# BiocWorkflowTools -## In both +
-* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘rcytoscapejs’ - ``` +* Version: 1.10.0 +* Source code: https://github.com/cran/BiocWorkflowTools +* Date/Publication: 2019-05-02 +* Number of recursive dependencies: 57 -# spectrolab +Run `revdep_details(,"BiocWorkflowTools")` for more info -Version: 0.0.7 +
## Newly broken -* checking whether package ‘spectrolab’ can be installed ... WARNING +* checking Rd cross-references ... WARNING ``` - Found the following significant warnings: - Warning: 'devtools::use_package' is deprecated. - See ‘.../revdep/checks.noindex/spectrolab/new/spectrolab.Rcheck/00install.out’ for details. + Missing link or links in documentation object 'createBiocWorkflow.Rd': + ‘create’ + + See section 'Cross-references' in the 'Writing R Extensions' manual. ``` ## In both @@ -3288,471 +56,197 @@ Version: 0.0.7 ``` Namespace in Imports field not imported from: ‘devtools’ All declared Imports should be used. + Unexported objects imported by ':::' calls: + ‘BiocStyle:::auth_affil_latex’ ‘BiocStyle:::modifyLines’ + ‘rmarkdown:::partition_yaml_front_matter’ + See the note in ?`:::` about the use of this operator. ``` -# spew - -Version: 1.3.0 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Loading required package: sp - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - no font could be found for family "10" - Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y, : - no font could be found for family "10" - Quitting from lines 45-64 (spew-quickstart.Rmd) - Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics: - polygon edge not found - Execution halted - ``` - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘Rmpi’ - ``` - -* checking dependencies in R code ... NOTE - ``` - Namespace in Imports field not imported from: ‘maptools’ - All declared Imports should be used. - ``` - -# SpidermiR - -Version: 1.10.0 +# googleAuthR -## In both +
-* checking package dependencies ... ERROR - ``` - Packages required but not available: ‘miRNAtap.db’ ‘org.Hs.eg.db’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. - ``` +* Version: 0.8.0 +* Source code: https://github.com/cran/googleAuthR +* URL: http://code.markedmondson.me/googleAuthR/ +* BugReports: https://github.com/MarkEdmondson1234/googleAuthR/issues +* Date/Publication: 2019-06-30 15:00:03 UTC +* Number of recursive dependencies: 88 -# StarBioTrek +Run `revdep_details(,"googleAuthR")` for more info -Version: 1.6.0 +
-## In both +## Newly broken -* checking package dependencies ... ERROR +* checking Rd cross-references ... WARNING ``` - Package required but not available: ‘org.Hs.eg.db’ + Missing link or links in documentation object 'gar_create_package.Rd': + ‘[devtools]{create}’ ‘[devtools]{use_github}’ - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + See section 'Cross-references' in the 'Writing R Extensions' manual. ``` -# sweep - -Version: 0.2.1.1 - ## In both * checking dependencies in R code ... NOTE ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’ + Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used. + Missing or unexported objects: + ‘devtools::create’ ‘devtools::use_github’ ``` -# syuzhet +# packagedocs -Version: 1.0.4 - -## In both +
-* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - R 1.3Mb - extdata 3.1Mb - ``` +* Version: 0.4.0 +* Source code: https://github.com/cran/packagedocs +* URL: http://hafen.github.io/packagedocs, https://github.com/hafen/packagedocs +* BugReports: https://github.com/hafen/packagedocs/issues +* Date/Publication: 2016-11-04 00:41:33 +* Number of recursive dependencies: 59 -# taxlist +Run `revdep_details(,"packagedocs")` for more info -Version: 0.1.5 +
-## In both +## Newly broken * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘grDevices’ - All declared Imports should be used. - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 97 marked UTF-8 strings + Missing or unexported objects: + ‘devtools::use_build_ignore’ ‘devtools::use_travis’ ``` -# TCGAbiolinks +# soilcarbon -Version: 2.8.4 +
-## In both +* Version: 1.2.0 +* Source code: https://github.com/cran/soilcarbon +* URL: https://powellcenter-soilcarbon.github.io/soilcarbon/ +* BugReports: https://github.com/powellcenter-soilcarbon/soilcarbon/issues +* Date/Publication: 2017-08-04 03:17:31 UTC +* Number of recursive dependencies: 86 -* R CMD check timed out - +Run `revdep_details(,"soilcarbon")` for more info -* checking dependencies in R code ... WARNING - ``` - '::' or ':::' import not declared from: ‘tidyr’ - ``` +
-* checking installed package size ... NOTE - ``` - installed size is 74.7Mb - sub-directories of 1Mb or more: - R 4.1Mb - data 3.9Mb - doc 66.4Mb - ``` +## Newly broken * checking R code for possible problems ... NOTE ``` - ... - TCGAvisualize_SurvivalCoxNET: no visible global function definition for - ‘dNetPipeline’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:161-162) - TCGAvisualize_SurvivalCoxNET: no visible global function definition for - ‘dCommSignif’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:174) - TCGAvisualize_SurvivalCoxNET: no visible global function definition for - ‘visNet’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:184-189) - TCGAvisualize_oncoprint: no visible binding for global variable ‘value’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/visualize.R:944) - readExonQuantification: no visible binding for global variable ‘exon’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/prepare.R:234-235) - readExonQuantification: no visible binding for global variable - ‘coordinates’ - (.../revdep/checks.noindex/TCGAbiolinks/new/TCGAbiolinks.Rcheck/00_pkg_src/TCGAbiolinks/R/prepare.R:234-235) + compileDatabase: no visible global function definition for ‘use_data’ + (.../revdep/checks.noindex/soilcarbon/new/soilcarbon.Rcheck/00_pkg_src/soilcarbon/R/compileDatabase.R:30) Undefined global functions or variables: - TabSubtypesCol_merged Tumor.purity barcode c3net clinical coordinates - dCommSignif dNetInduce dNetPipeline exon knnmi.cross - limmacontrasts.fit limmamakeContrasts minet portions rse_gene value - visNet + use_data ``` -# TCGAbiolinksGUI - -Version: 1.6.1 - ## In both -* checking package dependencies ... ERROR +* checking data for non-ASCII characters ... NOTE ``` - Packages required but not available: - ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ - ‘IlluminaHumanMethylation450kmanifest’ - ‘IlluminaHumanMethylation27kmanifest’ - ‘IlluminaHumanMethylation27kanno.ilmn12.hg19’ - ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ - ‘IlluminaHumanMethylationEPICmanifest’ - - See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ - manual. + Note: found 145 marked UTF-8 strings ``` -# TCGAutils - -Version: 1.0.1 - -## In both - -* checking re-building of vignette outputs ... WARNING - ``` - Error in re-building vignettes: - ... - Quitting from lines 16-22 (TCGAutils.Rmd) - Error: processing vignette 'TCGAutils.Rmd' failed with diagnostics: - there is no package called 'curatedTCGAData' - Execution halted - ``` +# SpaDES.core -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: ‘curatedTCGAData’ - ``` +
-* checking dependencies in R code ... NOTE - ``` - Unexported objects imported by ':::' calls: - ‘BiocGenerics:::replaceSlots’ ‘GenomicRanges:::.normarg_field’ - See the note in ?`:::` about the use of this operator. - ``` +* Version: 0.2.5 +* Source code: https://github.com/cran/SpaDES.core +* URL: http://spades-core.predictiveecology.org/, https://github.com/PredictiveEcology/SpaDES.core +* BugReports: https://github.com/PredictiveEcology/SpaDES.core/issues +* Date/Publication: 2019-03-19 05:43:37 UTC +* Number of recursive dependencies: 151 -# testthat +Run `revdep_details(,"SpaDES.core")` for more info -Version: 2.0.0 +
## Newly broken -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/test-catch.R’ failed. - Last 13 lines of output: - Calls: local ... with_rprofile_user -> with_envvar -> force -> force -> i.p - In addition: Warning messages: - 1: 'devtools::create' is deprecated. - Use 'usethis::create_package()' instead. - See help("Deprecated") and help("devtools-deprecated"). - 2: 'setup' is deprecated. - Use 'usethis::create_package()' instead. - See help("Deprecated") and help("devtools-deprecated"). - 3: 'create_description' is deprecated. - Use 'usethis::use_description()' instead. - See help("Deprecated") and help("devtools-deprecated"). - 4: 'use_rstudio' is deprecated. - Use 'usethis::use_rstudio()' instead. - See help("Deprecated") and help("devtools-deprecated"). - Execution halted - ``` - -# texmex - -Version: 2.4 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.1Mb - sub-directories of 1Mb or more: - R 1.6Mb - doc 3.2Mb - ``` - -# timetk - -Version: 0.1.1.1 - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - ‘devtools’ ‘forecast’ - All declared Imports should be used. - ``` - -# tosca - -Version: 0.1-2 - -## In both - * checking installed package size ... NOTE ``` - installed size is 5.8Mb + installed size is 5.6Mb sub-directories of 1Mb or more: - data 4.7Mb - ``` - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 1946 marked UTF-8 strings + R 3.1Mb + doc 1.6Mb ``` -# toxplot - -Version: 0.1.1 - ## In both -* checking dependencies in R code ... NOTE +* checking examples ... ERROR ``` - Namespace in Imports field not imported from: ‘tidyr’ - All declared Imports should be used. + ... + + .globals = list(stackName = "landscape", burnStats = "nPixelsBurned") + + ), + + modules = list("caribouMovement"), + + paths = list(modulePath = path) + + ) + Setting: + options( + spades.modulePath = '.../revdep/checks.noindex/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core/sampleModules' + ) + Paths set to: + options( + reproducible.cachePath = '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpvqUB3y/reproducible/cache' + spades.inputPath = '/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpUfXsOm/SpaDES/inputs' + spades.outputPath = '/private/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T/RtmpUfXsOm/SpaDES/outputs' + spades.modulePath = '.../revdep/checks.noindex/SpaDES.core/new/SpaDES.core.Rcheck/SpaDES.core/sampleModules' + ) + Warning in gzfile(file, mode) : + cannot open compressed file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/RtmpvqUB3y/reproducible/cache/.Require/_Users_jhester_Dropbox_projects_devtools_revdep_checks.noindex_SpaDES.core_new_SpaDES.core.Rcheck.snapshot.RDS', probable reason 'No such file or directory' + Error in gzfile(file, mode) : cannot open the connection + Calls: simInit ... Require -> installedVersionsQuick -> saveRDS -> gzfile + Execution halted ``` -# twoddpcr - -Version: 1.4.1 +* R CMD check timed out + -## In both +# understandBPMN -* checking installed package size ... NOTE - ``` - installed size is 6.4Mb - sub-directories of 1Mb or more: - data 1.2Mb - doc 4.1Mb - ``` +
-# UKgrid +* Version: 1.1.0 +* Source code: https://github.com/cran/understandBPMN +* Date/Publication: 2018-06-08 15:15:35 UTC +* Number of recursive dependencies: 72 -Version: 0.1.0 +Run `revdep_details(,"understandBPMN")` for more info -## In both +
-* checking installed package size ... NOTE - ``` - installed size is 12.0Mb - sub-directories of 1Mb or more: - data 3.6Mb - doc 8.3Mb - ``` +## Newly broken * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘rlang’ - All declared Imports should be used. + Missing or unexported object: ‘devtools::use_data’ ``` -# umx - -Version: 2.8.0 - -## In both +# zebu -* checking installed package size ... NOTE - ``` - installed size is 5.4Mb - sub-directories of 1Mb or more: - R 2.9Mb - help 2.2Mb - ``` +
-* checking Rd cross-references ... NOTE - ``` - Package unavailable to check Rd xrefs: ‘sem’ - ``` +* Version: 0.1.2 +* Source code: https://github.com/cran/zebu +* URL: http://github.com/oliviermfmartin/zebu +* BugReports: https://github.com/oliviermfmartin/zebu/issues +* Date/Publication: 2017-10-24 14:05:08 UTC +* Number of recursive dependencies: 80 -# unitizer +Run `revdep_details(,"zebu")` for more info -Version: 1.4.5 +
## Newly broken -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/runtt.R’ failed. - Last 13 lines of output: - + warning("Cannot run tests without `testthat` available") - + } - Loading required package: testthat - State tracking is disabled by default to comply with CRAN policies. Add `options(unitizer.state='recommended')` to your 'Rprofile' file to enable, or `options(unitizer.state='off')` to quash this message without enabling. See `?unitizerState` for details. - setup packages - Error in i.p(...) : - (converted from warning) installation of package '/var/folders/dt/r5s12t392tb5sk181j3gs4zw0000gn/T//Rtmp4lhiBZ/file1352dfa6605/unitizerdummypkg1_0.1.tar.gz' had non-zero exit status - Error in eval(quote({ : install error - Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval - Removing packages from '.../revdep/checks.noindex/unitizer/new/unitizer.Rcheck' - (as 'lib' is unspecified) - Error in find.package(pkgs, lib) : - there are no packages called 'unitizerdummypkg1', 'unitizerdummypkg2', 'utzflm' - Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval - Execution halted - ``` - -# unvotes - -Version: 0.2.0 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 4494 marked UTF-8 strings - ``` - -# veccompare - -Version: 0.1.0 - -## In both - * checking dependencies in R code ... NOTE ``` - Namespace in Imports field not imported from: ‘pander’ - All declared Imports should be used. - ``` - -# vegtable - -Version: 0.1.3 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 124 marked UTF-8 strings - ``` - -# Wats - -Version: 0.10.3 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 12.4Mb - sub-directories of 1Mb or more: - doc 12.1Mb - ``` - -# weathercan - -Version: 0.2.7 - -## In both - -* checking data for non-ASCII characters ... NOTE - ``` - Note: found 25 marked UTF-8 strings - ``` - -# workflowr - -Version: 1.1.1 - -## In both - -* checking tests ... - ``` - ERROR - Running the tests in ‘tests/testthat.R’ failed. - Last 13 lines of output: - remotes["origin"] == "https://github.com/fakename/fakerepo.git" isn't true. - - ── 5. Failure: wflow_git_remote can add a second remote. (@test-wflow_git_remote - remotes["upstream"] == "https://github.com/fake2/fakerepo2.git" isn't true. - - ══ testthat results ═══════════════════════════════════════════════════════════ - OK: 556 SKIPPED: 90 FAILED: 5 - 1. Failure: authenticate_git can create HTTPS credentials (@test-wflow_git_push_pull.R#144) - 2. Failure: authenticate_git can create HTTPS credentials (@test-wflow_git_push_pull.R#145) - 3. Failure: authenticate_git can create HTTPS credentials (@test-wflow_git_push_pull.R#146) - 4. Failure: wflow_git_remote can add a remote. (@test-wflow_git_remote.R#45) - 5. Failure: wflow_git_remote can add a second remote. (@test-wflow_git_remote.R#52) - - Error: testthat unit tests failed - Execution halted - ``` - -# wru - -Version: 0.1-7 - -## In both - -* checking installed package size ... NOTE - ``` - installed size is 5.8Mb - sub-directories of 1Mb or more: - data 5.6Mb + Missing or unexported object: ‘devtools::use_data’ ```