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cran-comments.md

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This is a resubmission, using the canonical link to the proto package.
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---
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## Test environments
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* OS X, R 3.2.2
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* Ubuntu 14.04, R 3.2.2
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* OS X, R 3.2.3
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* Ubuntu 14.04, R 3.2.3
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* win-builder (devel and release)
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## R CMD check results
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I think the problem is a poorly configured webserver:
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`curl http://fueleconomy.gov` works, but `curl -I http://fueleconomy.gov`
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(which sends a HEAD request) does not.
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## Reverse dependencies
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* I ran `R CMD check` on 674 all reverse dependencies
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(summary at https://github.com/hadley/ggplot2/blob/master/revdep/)
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* Maintainers with NOTEs, WARNINGs, or ERRORS were notified on Feb 10,
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and again on Feb 25. I have switched to a new automated system for
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maintainer notification, which ensures each maintainer gets a personalised
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email, and hopefully is more likely to take action.
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* I've also tried to give a more detailed breakdown of ERRORs/WARNINGs
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(but not NOTEs below). Please let me know if there's anything else I
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can do to make this more helpful.
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As far as I can tell, there are 3 failures related to changes to ggplot2:
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* ggtern: checking examples ... ERROR
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Caused by change in API. Author is aware but hasn't fixed.
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* plotly: checking tests ... ERROR
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Probably caused by changes to histogram API.
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* precrec: checking tests ... ERROR
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Using a bad test for class inheritance + minor change in ggplot2.
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There were a number of failures that don't appear to be related to changes in ggplot2.
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* archivist: checking examples ... ERROR
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Looks like ggplot2 2.0.0 problem.
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* BCEA: checking examples ... ERROR
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I failed to install R2jags.
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* bcrm: checking examples ... ERROR
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Another JAGS problem
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* biogram: checking examples ... ERROR
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ggplot2 2.0.0 problem - using invalid parameter.
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* doBy: checking running R code from vignettes ... ERROR
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Needs very latest version of nlme
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* dotwhisker: checking examples ... ERROR
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Needs to attach grid (ggplot2 2.0.0 problem)
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* emil: checking examples ... ERROR
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Needs very latest version of nlme
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* eyetrackingR: checking examples ... ERROR
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Needs suggested package (lme4) to run examples
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* fuzzyforest: checking examples ... ERROR
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Needs GO.db
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* geoknife: checking examples ... ERROR
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Random curl failure
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* ggdendro: checking Rd cross-references ... WARNING
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ggplot2 2.0.0 problem: links to help topic that no longer exists
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* ggthemes: checking tests ... ERROR
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Automated code style checking failure
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* HistData: checking examples ... ERROR
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Namespace problem
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* iNEXT: checking Rd cross-references ... WARNING
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ggplot2 2.0.0 problem: links to help topic that no longer exists
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* metaheur: checking for missing documentation entries ... ERROR
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Needs very latest version of nlme
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* mlr: checking examples ... ERROR
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Needs very latest version of nlme
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I've also updated my email address to hadley@rstudio.com
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* multitable: checking running R code from vignettes ... ERROR
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Needs lme4
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* preproviz: checking tests ... ERROR
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Needs very latest version of nlme
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* ryouready: checking examples ... ERROR
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Needs very latest version of nlme
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* Rz: checking dependencies in R code ... WARNING
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Namespace issues
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* SciencesPo: checking examples ... ERROR
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Pre-existing ggplot2 2.0.0 problems
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* sdmvspecies: checking for executable files ... WARNING
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Includes executable file
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* vcdExtra: checking examples ... ERROR
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Needs very latest version of nlme
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* vdmR: checking examples ... ERROR
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Not sure: internal grid error.
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Additionally, I:
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* Failed to install dependencies for: AFM, benchmarkme, clusterfly, demi,
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ibmdbR, lme4, metaMix, PKgraph, pmc, prcbench, rms, rstanarm, SeqFeatR,
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SpaDES, specmine, survMisc, toaster, vcfR
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## Downstream dependencies
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* Failed to install: abd, alm, arqas, ARTool, BACA, bamdit, bdscale, bdvis,
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benchmark, biomod2, bootnet, brainGraph, brms, BTSPAS, capm, caret,
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caretEnsemble, ChainLadder, classify, climwin, conformal, COPASutils,
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CosmoPhotoz, covmat, crmPack, Deducer, diveRsity, eeptools, erer, extracat,
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ez, FAOSTAT, fheatmap, geneSLOPE, gettingtothebottom, gitter, greport,
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hdnom, HistDAWass, HLMdiag, hyperSpec, IntegratedJM, interplot, ITEMAN, kobe,
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LANDD, learnstats, lmerTest, localgauss, LOGIT, ltbayes, marked, MergeGUI,
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merTools, Methplot, micromap, MissingDataGUI, mizer, morse, mosaic, MultiMeta,
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mwaved, ncappc, NeuralNetTools, NMF, nparACT, npregfast, OriGen, partialAR,
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PBImisc, pequod, Phxnlme, playwith, PlotPrjNetworks, pomp, PPtreeViz,
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predictmeans, PSAboot, qgraph, quadrupen, RcmdrPlugin.KMggplot2,
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RcmdrPlugin.MA, rddtools, refund, refund.shiny, RFmarkerDetector,
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robCompositions, RobustEM, robustlmm, RSA, RSDA, rstan, RStoolbox, rsvg,
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SCGLR, sdcMicro, seewave, SensMixed, sgd, simmr, sjPlot, snpEnrichment,
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sparkTable, spikeSlabGAM, spoccutils, strvalidator, tadaatoolbox, TcGSA,
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tigerstats, tigris, treemap, TriMatch, userfriendlyscience, varian, vmsbase
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* Maintainers were notified on Feb 10.
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I think the majority of these are because I'm not currently installing bioconductor packages. I hope to work on that in the future.

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