R devel - Apr 2018 - Base R examples that write to current working directory

>>>>> Henrik Bengtsson <henrik.bengtsson at 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
    > <ligges at 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=.
    >>>> 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 at r-project.org mailing list
    >>> https://stat.ethz.ch/mailman/listinfo/r-devel
    >> 
    >> 
    >> ______________________________________________
    >> R-devel at r-project.org mailing list
    >> https://stat.ethz.ch/mailman/listinfo/r-devel

    > ______________________________________________
    > R-devel at r-project.org mailing list
    > https://stat.ethz.ch/mailman/listinfo/r-devel

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 <maechler at
stat.math.ethz.ch>
wrote:
> >>>>> Henrik Bengtsson <henrik.bengtsson at 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
>     > <ligges at 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 at r-project.org mailing list
>     >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>     >>
>     >>
>     >> ______________________________________________
>     >> R-devel at r-project.org mailing list
>     >> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>     > ______________________________________________
>     > R-devel at r-project.org mailing list
>     > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


-- 
Gabriel Becker, Ph.D
Scientist
Bioinformatics and Computational Biology
Genentech Research

	[[alternative HTML version deleted]]

>>>>> Gabe Becker <becker.gabe at gene.com>
>>>>>     on Tue, 3 Apr 2018 21:16:12 -0700 writes:
    > 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.

Thank you very much, Gabe,

I've committed most of it now (to R-devel only, to be ported to
3.5.0 alpha, later).

There are some issues I've wanted to postpone and open for
discussion, e.g., here (on R-devel):

https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17403#c3  :

1) All(?) the file-based graphics devices have a default file
   name which resides in the current working directory,
   pdf(), postscript(), png(), ..., and pictex().

   We may think that this *default* should be changed, rather
   than the documentation, e.g., for pictex() , from
   "Rplots.tex" to  tempfile("Rplots.tex")

2) The write() function, for 30 years back compatibility with S,
   has a default  'file = "data"'

   Should we change the default to use "", the same as
   write.table() uses, or also something tempfile() based?


https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17403#c4  :

3)  prompt() and promptData()  [and possibly other prompt*()] :

   I did not apply your proposed changes here, see the
   R-bugzilla for reasoning.

   Still one may want to propose changing the default behavior
   from using the getwd() working directory to tempdir() instead.
   

Martin


    > On Tue, Apr 3, 2018 at 2:37 AM, Martin Maechler <maechler at
stat.math.ethz.ch>
    > wrote:

    >> >>>>> Henrik Bengtsson <henrik.bengtsson at
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
    >> > <ligges at 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



    > -- 
    > Gabriel Becker, Ph.D
    > Scientist
    > Bioinformatics and Computational Biology
    > Genentech Research