[R-pkg-devel] puzzling CRAN rejection

[Ben Bolker]

On 10/12/20 4:40 PM, Duncan Murdoch wrote:
> There's this one in 
> https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Windows/00check.log: 
> 
> 
>    Comparing 'lmer-1.Rout' to 'lmer-1.Rout.save' ...428d427
> < boundary (singular) fit: see ?isSingular
> 430d428
> < boundary (singular) fit: see ?isSingular
> 
> Those messages about the singular fit show up in
> 
> https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Windows/examples_and_tests/tests_i386/lmer-1.Rout 
> 
> 
> but not in
> 
> https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Windows/examples_and_tests/tests_i386/lmer-1.Rout.save 
> 
> 
> The difference also doesn't show up in the x64 versions of the files.

   OK, thanks.

   I did notice this in passing (I think), but I got confused by the 
format.  (Also, it doesn't even rise to the level of a NOTE ...)

   It took me a while to localize the problem (line numbers have to be 
computing _after_ throwing away the R header info, see source code of 
tools::Rdiff()).

    Having spent this long reading tea leaves, I think I'm going to 
write to the CRAN maintainers for clarification.

   * Refactoring all the tests to decrease the testing time 
significantly is certainly possible (at worst I can make a lot of stuff 
conditionally skipped on CRAN), but would be a nuisance that I'd rather 
save for the next release if possible.

   * Eliminating the two lines of variable output is easy, but it's 
mildly annoying to update the version number for this small a correction 
...

   Looks like from now on there will only be odd-numbered releases of 
lme4 on CRAN, since I seem guaranteed to make trivial errors with my 
first (odd-numbered) try each time and have to bump the version number 
when fixing them ...

    Ben Bolker


> 
> Duncan Murdoch
> 
> On 12/10/2020 4:03 p.m., Ben Bolker wrote:
>>     Before I risk wasting the CRAN maintainers' time with a query, can
>> anyone see what I'm missing here?  Everything I can see looks OK, with
>> the possible exception of the 'NA' result for "CRAN incoming
>> feasibility" on r-devel-windows-ix86+x86_64 (which surely isn't my 
>> fault???)
>>
>>     Any help appreciated, as always.
>>
>>     Ben Bolker
>>
>>
>>
>>
>> =====
>> Dear maintainer,
>>
>> package lme4_1.1-24.tar.gz does not pass the incoming checks
>> automatically, please see the following pre-tests:
>> Windows:
>> <https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Windows/00check.log> 
>>
>> Status: OK
>> Debian:
>> <https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Debian/00check.log> 
>>
>> Status: OK
>>
>> Last released version's CRAN status: ERROR: 2, NOTE: 5, OK: 5
>> See: <https://CRAN.R-project.org/web/checks/check_results_lme4.html>
>>
>> Last released version's additional issues:
>>     gcc-UBSAN 
>> <https://www.stats.ox.ac.uk/pub/bdr/memtests/gcc-UBSAN/lme4>
>>
>> CRAN Web: <https://cran.r-project.org/package=lme4>
>>
>> Please fix all problems and resubmit a fixed version via the webform.
>> If you are not sure how to fix the problems shown, please ask for help
>> on the R-package-devel mailing list:
>> <https://stat.ethz.ch/mailman/listinfo/r-package-devel>
>> If you are fairly certain the rejection is a false positive, please
>> reply-all to this message and explain.
>>
>> More details are given in the directory:
>> <https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/> 
>>
>> The files will be removed after roughly 7 days.
>>
>> *** Strong rev. depends ***: afex agRee altmeta aods3 arm ARTool bapred
>> bayesammi BayesLN BayesSenMC baystability BBRecapture BClustLonG BFpack
>> blme blmeco blocksdesign BradleyTerry2 buildmer cAIC4 car carcass cgam
>> chngpt ciTools clickR climwin CLME clusteredinterference clusterPower
>> CMatching cpr cvms DClusterm dfmeta DHARMa diagmeta difR doremi
>> eda4treeR EdSurvey effects embed epr ESTER ez faraway faux fence
>> finalfit fishmethods fullfact gamm4 geex GHap glmertree glmmEP GLMMRR
>> glmmsr glmmTMB GLMpack gorica groupedstats gtheory gvcR HelpersMG
>> HeritSeq hmi iccbeta IDmeasurer IMTest inferference influence.ME
>> intRvals isni jlctree joineRmeta joineRML JointModel jomo jstable
>> JWileymisc KenSyn lefko3 lmem.qtler LMERConvenienceFunctions lmerTest
>> lmSupport longpower LSAmitR macc MAGNAMWAR manymodelr MargCond marked
>> mbest MDMR mediation MEMSS merDeriv merTools meta metamisc metan
>> metaplus Metatron micemd MiRKAT misty mixAK MixedPsy MixMAP MixRF MLID
>> mlma mlmRev mlVAR MMeM multiDimBio multil
>>    evelTools MultiRR MultisiteMediation mumm mvMISE MXM nanny omics
>> OptimClassifier pamm panelr paramhetero PBImisc pbkrtest pcgen
>> pedigreemm Phenotype phyr piecewiseSEM Plasmode PLmixed powerbydesign
>> powerlmm predictmeans PrevMap prLogistic psfmi ptmixed qape r2mlm
>> raincin Rcmdr refund reghelper regplot REndo reproducer rewie RLRsim
>> robustBLME robustlmm rockchalk rosetta rpql rptR rr2 RRreg rsq rstanarm
>> rstap rties RVAideMemoire RVFam sae semEff siland simr sjstats skpr
>> SlaPMEG smicd SoyNAM SPCDAnalyze specr SPreFuGED squid stability
>> standardize statgenGxE statgenSTA StroupGLMM structree Surrogate
>> surrosurv swissMrP TcGSA themetagenomics tidygate tidyMicro tramME
>> tukeytrend userfriendlyscience varTestnlme VCA VetResearchLMM warpMix
>> WebPower welchADF WeMix
>>
>> Best regards,
>> CRAN teams' auto-check service
>>
>>
>> Flavor: r-devel-windows-ix86+x86_64
>> Check: CRAN incoming feasibility, Result: NA
>>     Maintainer: 'Ben Bolker <bbolker+lme4 using gmail.com>'
>>
>> Flavor: r-devel-windows-ix86+x86_64
>> Check: Overall checktime, Result: NOTE
>>     Overall checktime 23 min > 10 min
>>
>> Flavor: r-devel-linux-x86_64-debian-gcc
>> Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
>>     Maintainer: 'Ben Bolker <bbolker+lme4 using gmail.com>'
>>
>> ______________________________________________
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