[Bioc-devel] different generator for random integers in R-devel

Shepherd, Lori Lor|@Shepherd @end|ng |rom Ro@we||P@rk@org
Tue Mar 19 14:41:47 CET 2019

The R-devel builders were actually updated yesterday so in the build report later today you should be able to see the updated R-devel version  except on merida2 which we are not updating and will soon be retired for celaya2 mac builder.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Stadler, Michael <Michael.Stadler using fmi.ch>
Sent: Tuesday, March 19, 2019 9:37:03 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] different generator for random integers in R-devel

Dear maintainers of the BioC build system

I have a shy questions regarding R-devel versions on the build machines:

Currently, these use different versions of R-devel:
malbec2 | Linux ...   | R Under development (unstable) (2019-01-21 r75999)
tokay2  | Windows ... | R Under development (unstable) (2019-03-09 r76216)
merida2 | OS X ...    | R Under development (unstable) (2018-11-27 r75683)
celaya2 | OS X ...    | R Under development (unstable) (2019-01-22 r76000)

A recent change in R-devel
(mostly in r76160, see https://github.com/wch/r-source/commit/e4acfd1f240a42b3fc1474a4d97017114e4eb053)
has changed the behaviour of sample()
(see also https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=17494 and https://stat.ethz.ch/pipermail/r-devel/2018-September/076817.html).

In order to maintain backward compatibility, we are using RNGkind(..., sample.kind = "Rounding")
to temporarily fall back to the behaviour of R-3.5. However, this will cause an error on R-devel < r76160,
where RNGkind() does not yet understand the "sample.kind" argument (currently malbec2, merida2 and celaya2).

This will obviously resolve itself once R-devel gets updated on the build machines, latest upon release of BioC 3.9.
I am just curious whether R-devel will be updated on the builders before that, so this issue does not mask other
potential problems in our package (QuasR).


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