[R-pkg-devel] puzzling CRAN rejection

[Duncan Murdoch]

On 12/10/2020 5:17 p.m., Ben Bolker wrote:
> 
> 
> 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 ...)

Yes, failing to match saved test output should be a fatal error, but 
isn't marked as one.

> 
>     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()).

One of my favourite programs back in the days when I used Windows was 
Beyond Compare (https://www.scootersoftware.com/).  They've had a Mac 
version for a while now; it works well too (though I kind of prefer the 
old Windows UI a bit for some reason).  It made it really easy to find 
this difference, once I figured out which files to compare.  I didn't 
even recognize the line numbers in the CRAN report as line numbers at first.

>      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
> ...

I'd say a mismatch in saved output isn't a small problem, it's either a 
too-sensitive test or something serious.

Duncan Murdoch

> 
>     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>'
>>>
>>> ______________________________________________
>>> R-package-devel using r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>
>>