Re: [R-pkg-devel] Unusually long execution time for R.utils::gzip on r-devel-windows
FWIW, as far as I can tell, Sys.readlink() still doesn't handle
symlinks (or junction points) on Windows. Were you thinking of
normalizePath()? That does now resolve both symlinks and junction
points on Windows (courtesy of a lot of work from Tomas), although I
don't recall the exact versions in which support was introduced. But
that would still give you a more efficient way of detecting such files
on Windows.
Kevin
On Sat, Feb 17, 2024 at 3:21 AM Stefan Mayer
wrote:
>
>
> > On 17. Feb 2024, at 09:16, Henrik Bengtsson
> > wrote:
> >
> > I can confirm that this has to fixed in R.utils. This gist is that
> > R.utils does lots of validation of read/write permissions, and deep
> > down it rely on system("dir") as a fallback method. If this is down
> > toward dirname(tempdir()), then it'll find a lot of files, e.g.
> >
> > […]
> >
> > So, yeah, wow! I'll look into fixing this, probably by removing this
> > fallback approach, which is very rarely needed; it was added way back
> > when Sys.readlink() didn't cover all cases.
>
> Thanks for looking into this, Henrik! Feel free to let me know if I can help
> with anything.
>
> - Stefan
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Re: [R-pkg-devel] Unusually long execution time for R.utils::gzip on r-devel-windows
> On 17. Feb 2024, at 09:16, Henrik Bengtsson
> wrote:
>
> I can confirm that this has to fixed in R.utils. This gist is that
> R.utils does lots of validation of read/write permissions, and deep
> down it rely on system("dir") as a fallback method. If this is down
> toward dirname(tempdir()), then it'll find a lot of files, e.g.
>
> […]
>
> So, yeah, wow! I'll look into fixing this, probably by removing this
> fallback approach, which is very rarely needed; it was added way back
> when Sys.readlink() didn't cover all cases.
Thanks for looking into this, Henrik! Feel free to let me know if I can help
with anything.
- Stefan
__
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Re: [R-pkg-devel] Unusually long execution time for R.utils::gzip on r-devel-windows
I can confirm that this has to fixed in R.utils. This gist is that
R.utils does lots of validation of read/write permissions, and deep
down it rely on system("dir") as a fallback method. If this is down
toward dirname(tempdir()), then it'll find a lot of files, e.g.
[1] " Datenträger in Laufwerk D: ist Daten"
[2] " Volumeseriennummer: 1826-A193"
[3] ""
[4] " Verzeichnis von D:\\temp"
[5] ""
[6] "17.02.2024 09:06 ."
[7] "14.02.2024 03:36 0 cc6H4Sp5"
[8] "15.02.2024 03:46 0 cc6PwKb4"
[9] "15.02.2024 16:25 0 cc6RH27v"
[10] "16.02.2024 01:50 0 ccafzzMl"
...
[7] "09.02.2024 04:48 RtmpURWDbA"
[8] "14.02.2024 04:35 RtmpURWeVC"
[9] "15.02.2024 04:00 RtmpUrwhHU"
[ reached getOption("max.print") -- omitted 17165 entries ]
Time difference of 18.67841 secs
So, yeah, wow! I'll look into fixing this, probably by removing this
fallback approach, which is very rarely needed; it was added way back
when Sys.readlink() didn't cover all cases.
/Henrik
On Fri, Feb 16, 2024 at 9:24 PM Henrik Bengtsson
wrote:
>
> Author of R.utils here. I happen to investigate this too right now,
> because of extremely slow win-builder performance of R.rsp checks,
> which in turn depends on R.utils.
>
> It's not obvious to me why this happens on win-builder. I've noticed
> slower and slower win-builder/cran-incoming checks over the years,
> despite the code not changing. Right now, I'm investigating a piece of
> code that calls shell("dir") as a fallback to figure out if a file is
> a symbol link or not - it could be that that takes a very long time on
> win-builder.
>
> So, stay tuned ... I'll report back when I find something out.
>
> /Henrik
>
> On Fri, Feb 16, 2024 at 4:43 PM Stefan Mayer
> wrote:
> >
> > Dear list,
> >
> > I tried to submit an update to my R package imagefluency, but the update
> > does not pass the incoming checks automatically. The problem is that one of
> > the examples takes too long to execute – but only under Windows with the
> > development version of R (R Under development (unstable) (2024-02-15 r85925
> > ucrt)).
> >
> > I was able to pin down the problem to using R.utils::gzip(). I created a
> > test package that illustrates the problem: https://github.com/stm/ziptest
> > The package has two functions that zip a file given a file path. When using
> > R.utils::gzip() (function `gzipit()` in the test package), I get a NOTE
> > when checking the package using devtools::check_win_devel()
> >
> > * checking examples ... [55s] NOTE
> > Examples with CPU (user + system) or elapsed time > 10s
> >user system elapsed
> > gzipit 6.91 47.24 54.84
> >
> > There is no issue with utils::zip() (function `zipit()` in the test
> > package). Is this somehow a bug in R.utils::gzip(), or is there an issue
> > with the combination of Windows and r-devel?
> >
> > Best, Stefan
> >
> > __
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> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
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Re: [R-pkg-devel] Unusually long execution time for R.utils::gzip on r-devel-windows
Author of R.utils here. I happen to investigate this too right now,
because of extremely slow win-builder performance of R.rsp checks,
which in turn depends on R.utils.
It's not obvious to me why this happens on win-builder. I've noticed
slower and slower win-builder/cran-incoming checks over the years,
despite the code not changing. Right now, I'm investigating a piece of
code that calls shell("dir") as a fallback to figure out if a file is
a symbol link or not - it could be that that takes a very long time on
win-builder.
So, stay tuned ... I'll report back when I find something out.
/Henrik
On Fri, Feb 16, 2024 at 4:43 PM Stefan Mayer
wrote:
>
> Dear list,
>
> I tried to submit an update to my R package imagefluency, but the update does
> not pass the incoming checks automatically. The problem is that one of the
> examples takes too long to execute – but only under Windows with the
> development version of R (R Under development (unstable) (2024-02-15 r85925
> ucrt)).
>
> I was able to pin down the problem to using R.utils::gzip(). I created a test
> package that illustrates the problem: https://github.com/stm/ziptest
> The package has two functions that zip a file given a file path. When using
> R.utils::gzip() (function `gzipit()` in the test package), I get a NOTE when
> checking the package using devtools::check_win_devel()
>
> * checking examples ... [55s] NOTE
> Examples with CPU (user + system) or elapsed time > 10s
>user system elapsed
> gzipit 6.91 47.24 54.84
>
> There is no issue with utils::zip() (function `zipit()` in the test package).
> Is this somehow a bug in R.utils::gzip(), or is there an issue with the
> combination of Windows and r-devel?
>
> Best, Stefan
>
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