My submission from auto-check, and I'm not sure why because Windows and Debian checks both list "OK" and there are no unresolved problems on the CRAN status ...
My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min")
I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than the 'testthat' tests, none of the individual test files take longer than 15sec, although this is doubled because they have to be run on 386 and x64 ...)
An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit)
Can anyone confirm/support those guesses?
cheers
Ben Bolker
=====
Dear maintainer,
package lme4_1.1-26.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_1.1-26_20201122_184744/Windows/00check.log>
Status: OK
Debian:<https://win-builder.r-project.org/incoming_pretest/lme4_1.1-26_20201122_184744/Debian/00check.log>
Status: OK
Last released version's CRAN status: NOTE: 7, OK: 5
See:<https://CRAN.R-project.org/web/checks/check_results_lme4.html>
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_1.1-26_20201122_184744/>
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 BradleyTerry2 brokenstick buildmer cAIC4 car carcass cgam chngpt ciTools clickR climwin CLME clusteredinterference clusterPower CMatching cpr cvms DClusterm dfmeta DHARMa diagmeta difR doremi eda4treeR EdSurvey eefAnalytics effects eirm 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 inti intRvals isni jlctree joineRmeta joineRML JointModel jomo jstable JWileymisc KenSyn latrend lefko3 lmem.qtler LMERConvenienceFunctions lmerTest lmSupport longpower LSAmitR macc MAGNAMWAR manymodelr MargCond marked mbest MDMR mediation MEMSS merDeriv merTools meta metamicrobiomeR metamisc metan metaplus Metatron micemd MiRKAT misty mixAK MixedPsy MixMAP MixRF
MLID mlma mlmRev mlVAR MMeM multiDimBio multilevelTools MultiRR MultisiteMediation mumm mvMISE MXM nanny omics OptimClassifier packDAMipd pamm paramhetero PBImisc pbkrtest pcgen pedigreemm Phenotype phyr piecewiseSEM Plasmode PLmixed powerbydesign powerlmm predictmeans PrevMap prLogistic projpred psfmi ptmixed qape r2mlm raincin rbenvo 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 supernova Surrogate surrosurv swissMrP TcGSA themetagenomics tidyBF 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 18 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>'
[R-pkg-devel] help interpreting a response from CRAN
7 messages · Dirk Eddelbuettel, Ben Bolker, Roy Mendelssohn - NOAA Federal +1 more
On 22 November 2020 at 13:44, Ben Bolker wrote:
| My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
| I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than the 'testthat' tests, none of the individual test files take longer than 15sec, although this is doubled because they have to be run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch or, as
I do with test runner I use, exit_file("...") based on such conditions.
| An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
https://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to have real world examples. Small data and few iterations are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges
On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
On 22 November 2020 at 13:44, Ben Bolker wrote:
| My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
| I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than the 'testthat' tests, none of the individual test files take longer than 15sec, although this is doubled because they have to be run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch or, as
I do with test runner I use, exit_file("...") based on such conditions.
| An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
Thanks all for the help. The reward (as usual) is another dumb question. If I add up the elapsed times listed in https://win-builder.r-project.org/incoming_pretest/lme4_1.1-26_20201122_184744/Windows/examples_and_tests/examples_x64/lme4-Ex.timings I get 21.43 seconds. But the output in https://win-builder.r-project.org/incoming_pretest/lme4_1.1-26_20201122_184744/Windows/00check.log says ** running examples for arch 'x64' ... [41s] OK The values for i386 have a similar discrepancy (20.6 vs 36s). I can appreciate that would be a bit of overhead (and rounding error), but ... ? (there are a total of 61 examples) I wouldn't normally worry about the discrepancy, but I'm doing my best to shave seconds where I can ... can anyone see any obvious thinkos? I might as well add (in my partial defense, in response to Uwe's point about not needing real-world/big examples for tests); many of lme4's tests are regression tests of edge cases that came up in the real world with moderately sized data sets. *In principle* it might be possible to find a way to reduce those medium-sized problems to small, fast problems that still demonstrated the same numerical problems, but it's hard and time-consuming (at least for me) ... cheers Ben Bolker
On 11/22/20 4:06 PM, Uwe Ligges wrote:
Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to have real world examples. Small data and few iterations are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
On 22 November 2020 at 13:44, Ben Bolker wrote:
|??? My current guess is that the problem is with the too-long check
time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
|?? I guess I have to get busy setting more tests and examples to
skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other
than the 'testthat' tests, none of the individual test files take
longer than 15sec, although this is doubled because they have to be
run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch
or, as
I do with test runner I use, exit_file("...") based on such conditions.
|?? An alternative is that this is a confusingly worded message
indicating that there are strong rev dependencies so the package needs
to be further checked? (That seems unlikely as it explicitly asks me
to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
And one more (last for a while): presumably there is no way to check CRAN windows timing without submitting to CRAN ... ? (I will obviously do my best by doing arithmetic on the tests that I set to be skipped, but it would be nice to be able to double-check without wasting everyone's time ... I guess if I knew that CRAN submissions would *always automatically* be rejected with Windows test times>10 min, I could use CRAN submission itself as my test ... but maybe that's a bad idea?)
On 11/22/20 4:06 PM, Uwe Ligges wrote:
Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to have real world examples. Small data and few iterations are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
On 22 November 2020 at 13:44, Ben Bolker wrote:
|??? My current guess is that the problem is with the too-long check
time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
|?? I guess I have to get busy setting more tests and examples to
skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other
than the 'testthat' tests, none of the individual test files take
longer than 15sec, although this is doubled because they have to be
run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch
or, as
I do with test runner I use, exit_file("...") based on such conditions.
|?? An alternative is that this is a confusingly worded message
indicating that there are strong rev dependencies so the package needs
to be further checked? (That seems unlikely as it explicitly asks me
to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
I have found win-builder timings come close, but only close. My experience is that the CRAN timings were uniformly slower than those on win-builder. But I also find that I can get quite significant differences between win-builder-release and win-builder-devel. So I also take the slowest that I can find as a basis, and assume the actual times will be slower than that. HTH, -Roy
On Nov 22, 2020, at 5:15 PM, Ben Bolker <bbolker at gmail.com> wrote: And one more (last for a while): presumably there is no way to check CRAN windows timing without submitting to CRAN ... ? (I will obviously do my best by doing arithmetic on the tests that I set to be skipped, but it would be nice to be able to double-check without wasting everyone's time ... I guess if I knew that CRAN submissions would *always automatically* be rejected with Windows test times>10 min, I could use CRAN submission itself as my test ... but maybe that's a bad idea?) On 11/22/20 4:06 PM, Uwe Ligges wrote:
Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to have real world examples. Small data and few iterations are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
On 22 November 2020 at 13:44, Ben Bolker wrote:
| My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
| I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than the 'testthat' tests, none of the individual test files take longer than 15sec, although this is doubled because they have to be run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch or, as
I do with test runner I use, exit_file("...") based on such conditions.
| An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
On 23.11.2020 04:13, Roy Mendelssohn - NOAA Federal wrote:
I have found win-builder timings come close, but only close. My experience is that the CRAN timings were uniformly slower than those on win-builder. But I also find that I can get quite significant differences between win-builder-release and win-builder-devel. So I also take the slowest that I can find as a basis, and assume the actual times will be slower than that.
winbuilder and the WIndows check machione for the regul?ar checks are actually identical. Best, Uwe Ligges
HTH, -Roy
On Nov 22, 2020, at 5:15 PM, Ben Bolker <bbolker at gmail.com> wrote: And one more (last for a while): presumably there is no way to check CRAN windows timing without submitting to CRAN ... ? (I will obviously do my best by doing arithmetic on the tests that I set to be skipped, but it would be nice to be able to double-check without wasting everyone's time ... I guess if I knew that CRAN submissions would *always automatically* be rejected with Windows test times>10 min, I could use CRAN submission itself as my test ... but maybe that's a bad idea?) On 11/22/20 4:06 PM, Uwe Ligges wrote:
Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise. As a general remark for others who will read this in the future: tests should test the software, but it is generally not important to have real world examples. Small data and few iterations are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges On 22.11.2020 20:36, Dirk Eddelbuettel wrote:
On 22 November 2020 at 13:44, Ben Bolker wrote:
| My current guess is that the problem is with the too-long check time on Windows (NOTE: "Overall checktime 18 min > 10 min")
Yes.
| I guess I have to get busy setting more tests and examples to skip-on-CRAN (kind of a pain as there's no low-hanging fruit - other than the 'testthat' tests, none of the individual test files take longer than 15sec, although this is doubled because they have to be run on 386 and x64 ...)
It's under your control. You can detect 'are we on Windows' and branch or, as
I do with test runner I use, exit_file("...") based on such conditions.
| An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit)
No. If there were any (even false positive ones) they'd be listed there.
Hth, Dirk
______________________________________________ R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
********************** "The contents of this message do not reflect any position of the U.S. Government or NOAA." ********************** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new street address*** 110 McAllister Way Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: Roy.Mendelssohn at noaa.gov www: https://www.pfeg.noaa.gov/ "Old age and treachery will overcome youth and skill." "From those who have been given much, much will be expected" "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.