[R-pkg-devel] puzzling CRAN rejection

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 at 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 at gmail.com>'