Martin et al,
I have submitted a patch on bugzilla which fixes all of the examples I
could easily find which were not already writing only to temporary files or
switching to a temp directory before writing files to the working
directory. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17403
Passes make check-devel so the examples run and the packages that were
modified pass check.
Best,
~G
On Tue, Apr 3, 2018 at 2:37 AM, Martin Maechler <maech...@stat.math.ethz.ch>
wrote:
> >>>>> Henrik Bengtsson <henrik.bengts...@gmail.com>
> >>>>> on Fri, 30 Mar 2018 10:14:04 -0700 writes:
>
> > So, the proposal would then be to write to tempdir(),
> > correct? If so, I see three alternatives:
>
> > 1. explicitly use file.path(tempdir(), filename), or
> > tempfile() everywhere.
>
> I think it should clearly be '1.',
> as both '2.' and '3.' would need new functionality in R.
>
> Ideally we'd get the patch within a day or two, so we can safely
> apply it also to R 3.5.0 alpha (before it turns beta!).
>
> I think the 'eval.path' argument to example() is a nice idea,
> but also changing its default to tempdir() is definitely out of
> the question for R 3.5.0.
>
> Martin
>
>
> > 2. wrap example code in a withTempDir({ ... }) call.
>
> > 3. Add an 'eval.path' (*) argument to example() and make
> > it default to eval.path = tempdir(). This would probably
> > be backward compatible and keep the code example clean.
> > The downside is when a user runs an example and can't
> > locate produced files. (*) or 'wd', 'workdir', ...
>
> > /Henrik
>
> > On Fri, Mar 30, 2018 at 9:25 AM, Uwe Ligges
> > <lig...@statistik.tu-dortmund.de> wrote:
> >>
> >>
> >> On 30.03.2018 00:08, Duncan Murdoch wrote:
> >>>
> >>> On 29/03/2018 5:23 PM, Hadley Wickham wrote:
> >>>>
> >>>> Hi all,
> >>>>
> >>>> Given the recent CRAN push to prevent examples writing
> >>>> to the working directory, is there any interest in
> >>>> fixing base R examples that write to the working
> >>>> directory? A few candidates are the graphics devices,
> >>>> file.create(), writeBin(), writeChar(), write(), and
> >>>> saveRDS(). I'm sure there are many more.
> >>>>
> >>>> One way to catch these naughty examples would be to
> >>>> search for unlink() in examples: e.g.,
> >>>>
> >>>> https://github.com/wch/r-source/search?utf8=✓&q=unlink+
> extension%3ARd&type=
> <https://github.com/wch/r-source/search?utf8=%E2%9C%93&q=unlink+extension%3ARd&type=>
> .
> >>>> Of course, simply cleaning up after yourself is not
> >>>> sufficient because if those files existed before the
> >>>> examples were run, the examples will destroy them.
> >>>>
> >>>
> >>> Why not put together a patch that fixes these? This
> >>> doesn't seem to be something that needs discussion,
> >>> fixing the bad examples would be a good idea.
> >>
> >>
> >> Seconded. CRAN would not accept these base packages,
> >> hence we should urgently give better examples.
> >>
> >> Best, Uwe
> >>
> >>
> >>
> >>> Duncan Murdoch
> >>>
> >>> ______________________________________________
> >>> R-devel@r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >> ______________________________________________
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>
> > ______________________________________________
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>
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>
--
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research
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