Skip to content

Commit 7f04c25

Browse files
hadleyhadley
committed
Categorise problems
1 parent 1a2a5b1 commit 7f04c25

File tree

1 file changed

+163
-78
lines changed

1 file changed

+163
-78
lines changed

‎cran-comments.md

Lines changed: 163 additions & 78 deletions
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,6 @@
1-
This is a resubmission after fixing a bug that affect mlr and SciencePo.
2-
3-
---------------------------------
4-
5-
This is a resubmission, post-review of \dontrun{} usage. Now \dontrun{} is only used in two places: an example that fails on some platforms, and an ggsave() examples which save files on disk.
6-
7-
---------------------------------
8-
91
## Test environments
10-
* OS X, R 3.2.3
11-
* Ubuntu 14.04, R 3.2.3
2+
* OS X, R 3.3.1
3+
* Ubuntu 14.04, R 3.3.1
124
* win-builder (devel and release)
135

146
## R CMD check results
@@ -26,94 +18,187 @@ There were no ERRORs or WARNINGs. I see one NOTE:
2618

2719
## Reverse dependencies
2820

29-
* I ran `R CMD check` on 674 all reverse dependencies
21+
* I ran `R CMD check` on 954 all reverse dependencies
3022
(summary at https://github.com/hadley/ggplot2/blob/master/revdep/).
31-
I checked with the dev versions of ggplot2, scales, and gtable, in an
32-
effort to maximise problems found.
23+
24+
* Maintainers with NOTEs, WARNINGs, or ERRORS were notified on Oct 6,
25+
Oct 6, and again today.
3326

34-
* Maintainers with NOTEs, WARNINGs, or ERRORS were notified on Feb 10,
35-
and again on Feb 25. I have switched to a new automated system for
36-
maintainer notification, which ensures each maintainer gets a personalised
37-
email, and hopefully is more likely to take action.
27+
* There are a lot of WARNINGS/ERRORs, but I've carefully reviewed them
28+
all and as far as I can tell they are either deliberate changes to
29+
the ggplot2 API, or unrelated problems. I'm sorry there are so many -
30+
I don't know how to better encourage package authors to submit
31+
updates. Every maintainer has been personally emailed at least twice.
3832

39-
* I've also tried to give a more detailed breakdown of ERRORs/WARNINGs
33+
* I given a more detailed breakdown of ERRORs/WARNINGs
4034
(but not NOTEs below). Please let me know if there's anything else I
4135
can do to make this more helpful.
4236

43-
As far as I can tell, there are 3 failures related to changes to ggplot2:
44-
45-
* ggtern: checking examples ... ERROR
46-
Caused by change in API. Author is aware but hasn't fixed.
37+
### ggproto mistake
4738

48-
* plotly: checking tests ... ERROR
49-
Probably caused by changes to histogram API.
39+
I unfortunately made an implementation error in ggproto (the OO system that ggplot2 uses) that inadvertently introduced a build-time dependency on ggplot2. I've fixed the problem and added a clear error message, but to fix a number of downstream failures will require a rebuild of the following packages against the new version of ggplot2:
5040

51-
* precrec: checking tests ... ERROR
52-
Using a bad test for class inheritance + minor change in ggplot2.
41+
* ggrepel (GeomTextRepel)
42+
* ggmap (GeomRasterAnn)
43+
* ggpmisc (statpeaks)
44+
* ggbeeswarm (PositionQuasirandom)
5345

54-
There were a number of failures that don't appear to be related to changes in ggplot2.
46+
This problem affects the following downstream packgaes:
5547

5648
* archivist: checking examples ... ERROR
57-
Looks like ggplot2 2.0.0 problem.
58-
49+
* clustrd: checking examples ... ERROR
50+
* clifro: checking re-building of vignette outputs ... WARNING
51+
* corrr: checking examples ... ERROR
52+
* factoextra: checking examples ... ERROR
53+
* ggnetwork: checking examples ... ERROR
54+
* ggpmisc: checking examples ... ERROR
55+
* ggpubr: checking examples ... ERROR
56+
* idm: checking examples ... ERROR
57+
* OutbreakTools: checking examples ... ERROR
58+
* photobiologyInOut: checking re-building of vignette outputs ... WARNING
59+
* photobiologyLamps: checking re-building of vignette outputs ... WARNING
60+
* photobiologyLEDs: checking re-building of vignette outputs ... WARNING
61+
* photobiologyPlants: checking re-building of vignette outputs ... WARNING
62+
* SensusR: checking examples ... ERROR
63+
* sjPlot: checking examples ... ERROR
64+
* soc.ca: checking examples ... ERROR
65+
* trackeR: checking re-building of vignette outputs ... WARNING
66+
* vipor: checking re-building of vignette outputs ... WARNING
67+
68+
### ggplot2 changes
69+
70+
Need dev version of plotly: the maintainer is planning on submitting ASAP.
71+
72+
* eechidna: checking examples ... ERROR
73+
* heatmaply: checking examples ... ERROR
74+
* MendelianRandomization: checking examples ... ERROR
75+
* plotly: checking examples ... ERROR
76+
77+
Errors that were likely silently before, but now break thanks to stricter checks:
78+
79+
* biogram: checking re-building of vignette outputs ... WARNING
80+
* BlandAltmanLeh: checking re-building of vignette outputs ... WARNING
81+
* brms: checking tests ... ERROR
82+
* CopulaDTA: checking re-building of vignette outputs ... WARNING
83+
* ddpcr: checking re-building of vignette outputs ... WARNING
84+
* fheatmap: checking examples ... ERROR
85+
* gapfill: checking examples ... ERROR
86+
* ggExtra: checking examples ... ERROR
87+
* iNEXT: checking re-building of vignette outputs ... WARNING
88+
* largeVis: checking re-building of vignette outputs ... WARNING
89+
* MEGENA: checking re-building of vignette outputs ... WARNING
90+
* obAnalytics: checking examples ... ERROR
91+
* oddsratio: checking examples ... ERROR
92+
* onlineCPD: checking examples ... ERROR
93+
* PGRdup: checking re-building of vignette outputs ... WARNING
94+
* quickpsy: checking examples ... ERROR
95+
* sparkTable: checking examples ... ERROR
96+
* surveillance: checking re-building of vignette outputs ... WARNING
97+
* survMisc: checking examples ... ERROR
98+
* UpSetR: checking re-building of vignette outputs ... WARNING
99+
100+
Relying on ggplot2 internals, and haven't yet updated code for this version.
101+
102+
* geomnet: checking examples ... ERROR
103+
* GGally: checking examples ... ERROR
104+
* ggalt: checking examples ... ERROR
105+
* hyperSpec: checking examples ... ERROR
106+
* manhattanly: checking re-building of vignette outputs ... WARNING
107+
* mtconnectR: checking tests ... ERROR
108+
* quanteda: checking tests ... ERROR
109+
* rstanarm: checking examples ... ERROR
110+
* tabplot: checking examples ... ERROR
111+
* vdmR: checking examples ... ERROR
112+
113+
Uses newly deprecated argument
114+
115+
* plotluck: checking tests ... ERROR
116+
* robCompositions: checking re-building of vignette outputs ... WARNING
117+
118+
### Unrelated
119+
120+
Failed to installed suggested package used in examples or vignettes
121+
122+
* bcrm: checking examples ... ERROR
59123
* BCEA: checking examples ... ERROR
60-
I failed to install R2jags.
124+
* coloc: checking re-building of vignette outputs ... WARNING
125+
* emojifont: checking re-building of vignette outputs ... WARNING
126+
* fuzzyforest: checking examples ... ERROR
127+
* glycanr: checking examples ... ERROR
128+
* GenCAT: checking examples ... ERROR
129+
* ie2miscdata: checking re-building of vignette outputs ... WARNING
130+
* MixSIAR: checking examples ... ERROR
131+
* slim: checking re-building of vignette outputs ... WARNING
132+
* survminer: checking examples ... ERROR
133+
* tcgsaseq: checking examples ... ERROR
134+
* TELP: checking examples ... ERROR
61135

62-
* bcrm: checking examples ... ERROR
63-
Another JAGS problem
136+
Dependency of Hmisc on bleeding-edge survival:
64137

65-
* dotwhisker: checking examples ... ERROR
66-
Needs to attach grid (ggplot2 2.0.0 problem)
138+
* choroplethr: checking re-building of vignette outputs ... WARNING
139+
* Greg: checking examples ... ERROR
140+
* hdnom: checking examples ... ERROR
141+
* pander: checking re-building of vignette outputs ... WARNING
142+
* simcausal: checking re-building of vignette outputs ... WARNING
67143

68-
* emil: checking examples ... ERROR
69-
Needs very latest version of nlme
144+
Needs java:
70145

71-
* eyetrackingR: checking examples ... ERROR
72-
Needs suggested package (lme4) to run examples
146+
* mlr: checking examples ... ERROR
147+
* prcbench: checking examples ... ERROR
148+
* rfordummies: checking examples ... ERROR
149+
* userfriendlyscience: checking examples ... ERROR
73150

74-
* fuzzyforest: checking examples ... ERROR
75-
Needs GO.db
151+
Other/unknown:
76152

77-
* ggthemes: checking tests ... ERROR
78-
Automated code style checking failure
153+
* BioPET: checking examples ... ERROR
154+
Calling mean on non-numeric object
79155

80-
* iNEXT: checking Rd cross-references ... WARNING
81-
ggplot2 2.0.0 problem: links to help topic that no longer exists
156+
* ecb: checking tests ... ERROR
157+
Seems to be some badness in tests of remote server
82158

83-
* metaheur: checking for missing documentation entries ... ERROR
84-
Needs very latest version of nlme
159+
* fitbitScraper: checking re-building of vignette outputs ... WARNING
160+
Looks related to RCurl
85161

86-
* mlr: checking examples ... ERROR
87-
Needs very latest version of nlme
88-
89-
* multitable: checking running R code from vignettes ... ERROR
90-
Needs lme4
91-
92-
* preproviz: checking tests ... ERROR
93-
Needs very latest version of nlme
162+
* ggenealogy: checking re-building of vignette outputs ... WARNING
163+
Looks like encoding related issues in vignette
164+
165+
* ggfortify: checking tests ... ERROR
166+
Don't know what's causing these failures
167+
168+
* ParamHelpers: checking tests ... ERROR
169+
Failing test appears unrelated to ggplot2
170+
171+
* PredictTestbench: checking re-building of vignette outputs ... WARNING
172+
Missing `pred` arugment
173+
174+
* xtractomatic: checking re-building of vignette outputs ... WARNING
175+
Failed to open connection
176+
177+
Existing R CMD check failures:
94178

179+
* proportion: checking sizes of PDF files under ‘inst/doc’ ... WARNING
95180
* Rz: checking dependencies in R code ... WARNING
96-
Namespace issues
97-
98-
* sdmvspecies: checking for executable files ... WARNING
99-
Includes executable file
100-
101-
Additionally, I:
102-
103-
* Failed to install dependencies for: AFM, clusterfly, demi, ibmdbR, metaMix,
104-
PKgraph, pmc, prcbench, SeqFeatR, SpaDES, specmine, toaster
105-
106-
* Failed to install: abd, alm, arqas, ARTool, BACA, bamdit, bdscale, bdvis,
107-
benchmark, biomod2, brainGraph, brms, BTSPAS, capm, caret, caretEnsemble,
108-
ChainLadder, classify, conformal, COPASutils, crmPack, extracat, FAOSTAT,
109-
fheatmap, geneSLOPE, gettingtothebottom, gitter, granovaGG, HistDAWass,
110-
hyperSpec, IntegratedJM, kobe, LANDD, localgauss, LOGIT, ltbayes, MergeGUI,
111-
Methplot, micromap, MissingDataGUI, mizer, morse, MultiMeta, mwaved, ncappc,
112-
NeuralNetTools, NMF, nparACT, npregfast, OriGen, partialAR, patPRO, Phxnlme,
113-
playwith, PlotPrjNetworks, pomp, PPtreeViz, primerTree, quadrupen,
114-
refund.shiny, RobustEM, RSA, RSDA, rstan, rstanarm, RStoolbox, rsvg, SCGLR,
115-
seewave, sgd, simmr, sjPlot, snpEnrichment, sparkTable, spikeSlabGAM,
116-
spoccutils, strvalidator, tadaatoolbox, tigerstats, tigris, treemap,
117-
userfriendlyscience, vmsbase
118-
119-
I think the majority of these are because I'm not currently installing bioconductor packages. I hope to work on that in the future.
181+
* simmer: checking compiled code ... WARNING
182+
183+
Failed to install dependencies for: aop, BACA, cate, clusterfly, demi, gitter,
184+
gridDebug, Hmisc, HTSSIP, ibmdbR, IntClust, LANDD, LDheatmap, MetaIntegrator,
185+
metaMix, multiDimBio, myTAI, NFP, PKgraph, PlasmaMutationDetector, pRF, PSCBS,
186+
raptr, rms, RPPanalyzer, scmamp, SeqFeatR, snpEnrichment, specmine, starmie,
187+
structSSI, TcGSA, toaster
188+
189+
Failed to install: BACCT, backShift, bamdit, brainGraph, bsam, BTSPAS,
190+
classify, CollapsABEL, crmPack, Crossover, Deducer, DiversityOccupancy,
191+
DynNom, dynr, Fgmutils, funModeling, G2Sd, ggtern, greport, IAPWS95,
192+
imageData, imager, InSilicoVA, llama, localgauss, ltbayes, magick,
193+
MergeGUI, MissingDataGUI, morse, mrMLM, mwaved, npregfast, OpenStreetMap,
194+
openVA, OriGen, pcaPA, pcrsim, playwith, PortfolioEffectHFT, qdap, ReporteRs,
195+
RJafroc, rmcfs, rrepast, RSA, rstan, rsvg, SEERaBomb, seewave, simmr, spcosa,
196+
StroupGLMM, strvalidator, subspaceMOA, UBL, UsingR, vmsbase, x.ent, XGR,
197+
XLConnect
198+
199+
### False positives
200+
201+
These seem to be false positives: neither I nor the maintainers could reproduce outside of my revdep check setup.
202+
203+
* radiant.model: checking examples ... ERROR
204+
* data.table: checking tests ... ERROR

0 commit comments

Comments
 (0)