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From Felix Cheung <felixcheun...@hotmail.com>
Subject Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0
Date Thu, 08 Nov 2018 08:43:50 GMT
They were discussed on dev@ in Mar 2018, for example.

Several attempts were made in 2.3.0, 2.3.1, 2.3.2, 2.4.0.
It’s not just tests, the last one is with vignettes.

The current doc about RStudio actually assumes you have the full Spark distribution (ie from
the download page and Apache Mirror) and set SPARK_HOME etc, which is not a hard way and the
doc also says it is the same for R shell, R script or other R IDE, with the exact same steps.



________________________________
From: Matei Zaharia <matei.zaharia@gmail.com>
Sent: Wednesday, November 7, 2018 10:32 PM
To: Wenchen Fan
Cc: Shivaram Venkataraman; Felix Cheung; Sean Owen; Spark dev list
Subject: Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0

I didn’t realize the same thing was broken in 2.3.0, but we should probably have made this
a blocker for future releases, if it’s just a matter of removing things from the test script.
We should also make the docs at https://spark.apache.org/docs/latest/sparkr.html clear about
how we want people to run SparkR. They don’t seem to say to use any specific mirror or anything
(in fact they only talk about how to import SparkR in RStudio and in our bin/sparkR, not in
a normal R shell). I’m pretty sure it’s OK to update the docs website for 2.4.0 after
the release to fix this if we want.

Matei

> On Nov 7, 2018, at 6:24 PM, Wenchen Fan <cloud0fan@gmail.com> wrote:
>
> Do we need to create a JIRA ticket for it and list it as a known issue in 2.4.0 release
notes?
>
> On Wed, Nov 7, 2018 at 11:26 PM Shivaram Venkataraman <shivaram@eecs.berkeley.edu>
wrote:
> Agree with the points Felix made.
>
> One thing is that it looks like the only problem is vignettes and the
> tests are being skipped as designed. If you see
> https://win-builder.r-project.org/incoming_pretest/SparkR_2.4.0_20181105_165757/Windows/00check.log
> and https://win-builder.r-project.org/incoming_pretest/SparkR_2.4.0_20181105_165757/Debian/00check.log,
> the tests run in 1s.
> On Tue, Nov 6, 2018 at 1:29 PM Felix Cheung <felixcheung_m@hotmail.com> wrote:
> >
> > I’d rather not mess with 2.4.0 at this point. On CRAN is nice but users can also
install from Apache Mirror.
> >
> > Also I had attempted and failed to get vignettes not to build, it was non trivial
and could t get it to work. It I have an idea.
> >
> > As for tests I don’t know exact why is it not skipped. Need to investigate but
worse case test_package can run with 0 test.
> >
> >
> >
> > ________________________________
> > From: Sean Owen <srowen@gmail.com>
> > Sent: Tuesday, November 6, 2018 10:51 AM
> > To: Shivaram Venkataraman
> > Cc: Felix Cheung; Wenchen Fan; Matei Zaharia; dev
> > Subject: Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0
> >
> > I think the second option, to skip the tests, is best right now, if
> > the alternative is to have no SparkR release at all!
> > Can we monkey-patch the 2.4.0 release for SparkR in this way, bless it
> > from the PMC, and release that? It's drastic but so is not being able
> > to release, I think.
> > Right? or is CRAN not actually an important distribution path for
> > SparkR in particular?
> >
> > On Tue, Nov 6, 2018 at 12:49 PM Shivaram Venkataraman
> > <shivaram@eecs.berkeley.edu> wrote:
> > >
> > > Right - I think we should move on with 2.4.0.
> > >
> > > In terms of what can be done to avoid this error there are two strategies
> > > - Felix had this other thread about JDK 11 that should at least let
> > > Spark run on the CRAN instance. In general this strategy isn't
> > > foolproof because the JDK version and other dependencies on that
> > > machine keep changing over time and we dont have much control over it.
> > > Worse we also dont have much control
> > > - The other solution is to not run code to build the vignettes
> > > document and just have static code blocks there that have been
> > > pre-evaluated / pre-populated. We can open a JIRA to discuss the
> > > pros/cons of this ?
> > >
> > > Thanks
> > > Shivaram
> > >
> > > On Tue, Nov 6, 2018 at 10:57 AM Felix Cheung <felixcheung_m@hotmail.com>
wrote:
> > > >
> > > > We have not been able to publish to CRAN for quite some time (since 2.3.0
was archived - the cause is Java 11)
> > > >
> > > > I think it’s ok to announce the release of 2.4.0
> > > >
> > > >
> > > > ________________________________
> > > > From: Wenchen Fan <cloud0fan@gmail.com>
> > > > Sent: Tuesday, November 6, 2018 8:51 AM
> > > > To: Felix Cheung
> > > > Cc: Matei Zaharia; Sean Owen; Spark dev list; Shivaram Venkataraman
> > > > Subject: Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0
> > > >
> > > > Do you mean we should have a 2.4.0 release without CRAN and then do a
2.4.1 immediately?
> > > >
> > > > On Wed, Nov 7, 2018 at 12:34 AM Felix Cheung <felixcheung_m@hotmail.com>
wrote:
> > > >>
> > > >> Shivaram and I were discussing.
> > > >> Actually we worked with them before. Another possible approach is
to remove the vignettes eval and all test from the source package... in the next release.
> > > >>
> > > >>
> > > >> ________________________________
> > > >> From: Matei Zaharia <matei.zaharia@gmail.com>
> > > >> Sent: Tuesday, November 6, 2018 12:07 AM
> > > >> To: Felix Cheung
> > > >> Cc: Sean Owen; dev; Shivaram Venkataraman
> > > >> Subject: Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0
> > > >>
> > > >> Maybe it’s wroth contacting the CRAN maintainers to ask for help?
Perhaps we aren’t disabling it correctly, or perhaps they can ignore this specific failure.
+Shivaram who might have some ideas.
> > > >>
> > > >> Matei
> > > >>
> > > >> > On Nov 5, 2018, at 9:09 PM, Felix Cheung <felixcheung_m@hotmail.com>
wrote:
> > > >> >
> > > >> > I don¡Št know what the cause is yet.
> > > >> >
> > > >> > The test should be skipped because of this check
> > > >> > https://github.com/apache/spark/blob/branch-2.4/R/pkg/inst/tests/testthat/test_basic.R#L21
> > > >> >
> > > >> > And this
> > > >> > https://github.com/apache/spark/blob/branch-2.4/R/pkg/inst/tests/testthat/test_basic.R#L57
> > > >> >
> > > >> > But it ran:
> > > >> > callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper",
"fit", formula,
> > > >> >
> > > >> > The earlier release was achived because of Java 11+ too so this
unfortunately isn¡Št new.
> > > >> >
> > > >> >
> > > >> > From: Sean Owen <srowen@gmail.com>
> > > >> > Sent: Monday, November 5, 2018 7:22 PM
> > > >> > To: Felix Cheung
> > > >> > Cc: dev
> > > >> > Subject: Re: [CRAN-pretest-archived] CRAN submission SparkR 2.4.0
> > > >> >
> > > >> > What can we do to get the release through? is there any way to
> > > >> > circumvent these tests or otherwise hack it? or does it need
a
> > > >> > maintenance release?
> > > >> > On Mon, Nov 5, 2018 at 8:53 PM Felix Cheung <felixcheung_m@hotmail.com>
wrote:
> > > >> > >
> > > >> > > FYI. SparkR submission failed. It seems to detect Java 11
correctly with vignettes but not skipping tests as would be expected.
> > > >> > >
> > > >> > > Error: processing vignette ¡¥sparkr-vignettes.Rmd¡Š
failed with diagnostics:
> > > >> > > Java version 8 is required for this package; found version:
11.0.1
> > > >> > > Execution halted
> > > >> > >
> > > >> > > * checking PDF version of manual ... OK
> > > >> > > * DONE
> > > >> > > Status: 1 WARNING, 1 NOTE
> > > >> > >
> > > >> > > Current CRAN status: ERROR: 1, OK: 1
> > > >> > > See: <https://CRAN.R-project.org/web/checks/check_results_SparkR.html>
> > > >> > >
> > > >> > > Version: 2.3.0
> > > >> > > Check: tests, Result: ERROR
> > > >> > > Running ¡¥run-all.R¡Š [8s/35s]
> > > >> > > Running the tests in ¡¥tests/run-all.R¡Š failed.
> > > >> > > Last 13 lines of output:
> > > >> > > 4: callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper",
"fit", formula,
> > > >> > > data@sdf, tolower(family$family), family$link, tol, as.integer(maxIter),
weightCol,
> > > >> > > regParam, as.double(var.power), as.double(link.power), stringIndexerOrderType,
> > > >> > > offsetCol)
> > > >> > > 5: invokeJava(isStatic = TRUE, className, methodName, ...)
> > > >> > > 6: handleErrors(returnStatus, conn)
> > > >> > > 7: stop(readString(conn))
> > > >> > >
> > > >> > > ùùùù testthat results ùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùùù
> > > >> > > OK: 0 SKIPPED: 0 FAILED: 2
> > > >> > > 1. Error: create DataFrame from list or data.frame (@test_basic.R#26)
> > > >> > > 2. Error: spark.glm and predict (@test_basic.R#58)
> > > >> > >
> > > >> > >
> > > >> > >
> > > >> > > ---------- Forwarded message ---------
> > > >> > > Date: Mon, Nov 5, 2018, 10:12
> > > >> > > Subject: [CRAN-pretest-archived] CRAN submission SparkR
2.4.0
> > > >> > >
> > > >> > > Dear maintainer,
> > > >> > >
> > > >> > > package SparkR_2.4.0.tar.gz does not pass the incoming checks
automatically, please see the following pre-tests:
> > > >> > > Windows: <https://win-builder.r-project.org/incoming_pretest/SparkR_2.4.0_20181105_165757/Windows/00check.log>
> > > >> > > Status: 1 NOTE
> > > >> > > Debian: <https://win-builder.r-project.org/incoming_pretest/SparkR_2.4.0_20181105_165757/Debian/00check.log>
> > > >> > > Status: 1 WARNING, 1 NOTE
> > > >> > >
> > > >> > > Last released version's CRAN status: ERROR: 1, OK: 1
> > > >> > > See: <https://CRAN.R-project.org/web/checks/check_results_SparkR.html>
> > > >> > >
> > > >> > > CRAN Web: <https://cran.r-project.org/package=SparkR>
> > > >> > >
> > > >> > > 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/SparkR_2.4.0_20181105_165757/>
> > > >> > > The files will be removed after roughly 7 days.
> > > >> > >
> > > >> > > No strong reverse dependencies to be checked.
> > > >> > >
> > > >> > > Best regards,
> > > >> > > CRAN teams' auto-check service
> > > >> > > Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
> > > >> > > Check: CRAN incoming feasibility, Result: NOTE
> > > >> > > Maintainer: 'Shivaram Venkataraman <shivaram@cs.berkeley.edu>'
> > > >> > >
> > > >> > > New submission
> > > >> > >
> > > >> > > Package was archived on CRAN
> > > >> > >
> > > >> > > Possibly mis-spelled words in DESCRIPTION:
> > > >> > > Frontend (4:10, 5:28)
> > > >> > >
> > > >> > > CRAN repository db overrides:
> > > >> > > X-CRAN-Comment: Archived on 2018-05-01 as check problems
were not
> > > >> > > corrected despite reminders.
> > > >> > >
> > > >> > > Flavor: r-devel-linux-x86_64-debian-gcc
> > > >> > > Check: re-building of vignette outputs, Result: WARNING
> > > >> > > Error in re-building vignettes:
> > > >> > > ...
> > > >> > >
> > > >> > > Attaching package: 'SparkR'
> > > >> > >
> > > >> > > The following objects are masked from 'package:stats':
> > > >> > >
> > > >> > > cov, filter, lag, na.omit, predict, sd, var, window
> > > >> > >
> > > >> > > The following objects are masked from 'package:base':
> > > >> > >
> > > >> > > as.data.frame, colnames, colnames<-, drop, endsWith,
> > > >> > > intersect, rank, rbind, sample, startsWith, subset, summary,
> > > >> > > transform, union
> > > >> > >
> > > >> > > trying URL 'http://mirror.klaus-uwe.me/apache/spark/spark-2.4.0/spark-2.4.0-bin-hadoop2.7.tgz'
> > > >> > > Content type 'application/octet-stream' length 227893062
bytes (217.3 MB)
> > > >> > > ==================================================
> > > >> > > downloaded 217.3 MB
> > > >> > >
> > > >> > > Quitting from lines 65-67 (sparkr-vignettes.Rmd)
> > > >> > > Error: processing vignette 'sparkr-vignettes.Rmd' failed
with diagnostics:
> > > >> > > Java version 8 is required for this package; found version:
11.0.1
> > > >> > > Execution halted
> > > >>


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