I ahven't looked at you package, but can you please verify:
1. If you open some (socket) cluster, make sure you close it afterwards!
This is a very frequent source of problems.
2. Do not use more than 2 cores by default.
3. retry whether you pass the winbuilder checks, it could have been a
random error. How long does processing your vignettes take?
Best,
Uwe Ligges
On 24.04.2017 05:43, Jeremy Volkening wrote:
Henrik,
A completely different alternative, is to have a way to disable
parallel processing in your examples / tests / vignettes, e.g. if (np
== 1) registerDoSEQ() else registerDoParallel(np). Personally, I'm
not a big fan of that approach because it's an ad-hoc workaround and
you're end up not testing all of your package.
Supporting parallel processing has already caused me untold headaches as
a not-overly-fluent R user (including over an hour on Friday try to
figure out why my Windows tests were hanging indefinitely -- had to add
"Sys.unsetenv("R_TESTS") to the top of my test script which I still
don't understand). However, I would consider it an important feature of
the package where actual usage typically involves modeling data from
thousands of proteins, each of which can be bootstrapped up to 20
times. For this reason, I also don't like the idea of "testing around"
the issue. While I don't use Windows myself, it doesn't make sense to
claim my package runs on Windows if it is going to randomly freeze up
for users on that platform.
I will ask Uwe Ligges to re-check my submission as you suggested. I
would really like to get this past the pre-check stage so I can start
dealing with the issues that I'm sure will come up in the human review.
Regards,
Jeremy
Hope this helps
Henrik
On Sun, Apr 23, 2017 at 9:17 AM, Jeremy Volkening <j...@base2bio.com>
wrote:
On Sun, Apr 23, 2017 at 10:17:01AM +0200, Alexandre Courtiol wrote:
Could it be that one your computer you can build vignettes quickly
thanks
to some caching of the knitr chunk output but that it takes too much
time
building that without the cache...? ... CRAN does not like when
anything takes more than a few seconds...
Thanks for the reply. The vignettes do take a little time to build,
as the
knitr code is doing some modeling, but I wouldn't have thought it
excessive.
According to the logs from the win-builder service, it took 28s
(about the
same as each of the i386 and x64 tests). Is this too long for the CRAN
submission service? I've already pruned down my example data to just a
couple of samples instead of the thousands normally modeled in a
session.
If this is indeed the issue, do I need to remove the knitr code and just
include static images of the output plots in the vignette? This would
seem
to go against most of the recommendations I have read from various
sources
on best practice.
Regards,
Jeremy
On 23 April 2017 at 05:08, Jeremy Volkening <j...@base2bio.com> wrote:
Hello,
I am trying to submit a package to CRAN for the first time. I have
gone
through testing on my own machines (Linux, Windows x64, Windows
i386), on
Travis CI and using win-builder. All tests are now passing on all of
these
platforms. However, when I try to submit the package to CRAN I get an
email
that the pre-test has failed, with the following line:
Status: NA (check log incomplete, web timeout?)
The pre-test link is here: https://win-builder.r-project.
org/incoming_pretest/170423_044521_mstherm_047/
If I check the '00check.log' file I can see that it ends with the
line "*
checking re-building of vignette outputs ...", so apparently the
test is
quitting before it finishes this step. I'm not sure how to proceed,
since
everything is working for all of my own manual tests (as well as
win-builder). See the log for my manual submission of exactly the same
package to win-builder, which passes:
https://win-builder.r-project.org/4tvH1D2TdMep/
Any help would be greatly appreciated. The package itself can be found
here:
https://github.com/jvolkening/r-mstherm
Regards,
Jeremy
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--
Alexandre Courtiol
http://sites.google.com/site/alexandrecourtiol/home
*"Science is the belief in the ignorance of experts"*, R. Feynman
--
Nothing so needs reforming as other people's habits.
-- Mark Twain, "Pudd'nhead Wilson's Calendar"
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