From therne@u @end|ng |rom m@yo@edu  Thu Mar 28 15:22:10 2019
From: therne@u @end|ng |rom m@yo@edu (Therneau, Terry M., Ph.D.)
Date: Thu, 28 Mar 2019 09:22:10 -0500
Subject: [Rd] [EXTERNAL] Re:  issue with latest release of R-devel
In-Reply-To: <CAFDcVCQaHRXJkNaMo7UfU47ysOKdf7pB8uVD5aC9EMKnsNvXdQ@mail.gmail.com>
References: <b23057$bd0b8c@ironport10.mayo.edu>
 <CAFDcVCQaHRXJkNaMo7UfU47ysOKdf7pB8uVD5aC9EMKnsNvXdQ@mail.gmail.com>
Message-ID: <b23057$bd2h5o@ironport10.mayo.edu>

I have not yet checked all instances, but Henrik's suggestion is 3 for 3 so far.
Should I send notes to the packages in question, or will they get some from CRAN?

Terry


On 3/27/19 10:44 PM, Henrik Bengtsson wrote:
> Could this be related to
>
> "SIGNIFICANT USER-VISIBLE CHANGES
>
> The default method for generating from a discrete uniform distribution
> (used in sample(), for instance) has been changed. This addresses the
> fact, pointed out by Ottoboni and Stark, that the previous method made
> sample() noticeably non-uniform on large populations. See PR#17494 for
> a discussion. The previous method can be requested using RNGkind() or
> RNGversion() if necessary for reproduction of old results. Thanks to
> Duncan Murdoch for contributing the patch and Gabe Becker for further
> assistance."
>
> If so, testing with
>
>     export _R_RNG_VERSION_=3.5.0
>
> might remove/explain those errors.
>
> Just a thought
>
> Henrik
>
> On Wed, Mar 27, 2019 at 8:16 PM Therneau, Terry M., Ph.D. via R-devel
> <r-devel at r-project.org> wrote:
>> I'm getting ready to submit an update of survival, and is my habit I run the checks on all
>> packages that depend/import/suggest  survival.  I am getting some very odd behaviour wrt
>> non-reproducability.  It came to a head when some things failed on one machine and worked
>> on another.   I found that the difference was that the failure was using the 3/27 release
>> and the success was still on a late Jan release.   When I updated R on the latter machine
>> it now fails too.
>>
>> An example is the test cases in genfrail.Rd, in the frailtySurv package.   (The package
>> depends on survival, but I'm fairly sure that this function does not.)   It's a fairly
>> simple function to generate test data sets, with a half dozen calls in the test file.  If
>> you cut and paste the whole batch into an R session, the last one of them fails.  But if
>> you run that call by itself it works.   This yes/no behavior is reproducable.
>>
>> Another puzzler was the ranger package.  In the tests/testthat directory,
>> source('test_maxstat') fails if it is preceeded by source('test_jackknife'), but not
>> otherwise.  Again, I don't think the survival package is implicated in either of these tests.
>>
>> Another package that succeeded under the older r-devel and now fails is arsenal, but I
>> haven't looked deeply at that.
>>
>> Any insight would be be appreciated.
>>
>> Terry T.
>> ----
>>
>>
>> Here is the sessionInfo() for one of the machines.  The other is running xubuntu 18 LTS.
>> (It's at the office, and I can send that tomorrow when I get in.)
>>
>> R Under development (unstable) (2019-03-28 r76277)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.6 LTS
>>
>> Matrix products: default
>> BLAS:   /usr/local/src/R-devel/lib/libRblas.so
>> LAPACK: /usr/local/src/R-devel/lib/libRlapack.so
>>
>> locale:
>>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C
>>    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>    [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods base
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.0
>>
>>
>>          [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] [EXTERNAL] Re: issue with latest release of R-devel
Therneau, Terry M., Ph.D.