Re: [R] Zoo seems to be running slow in R 2.8.0 windows

From: stephen sefick <ssefick_at_gmail.com>
Date: Tue, 04 Nov 2008 13:06:58 -0500

this should be right- I have looked at it with summaryRprof() and it is spending most of its time on things I would expect... read.production and read.zoo. Is this the best way to communicate the results? Or do you want it copy and pasted into the email? thank you very much

On Tue, Nov 4, 2008 at 1:01 PM, Gabor Grothendieck <ggrothendieck_at_gmail.com> wrote:
> Here is the output:
>
>> summaryRprof()
> $by.self
> self.time self.pct total.time total.pct
> index.search 0.30 55.6 0.30 55.6
> .C 0.18 33.3 0.18 33.3
> inDL 0.06 11.1 0.06 11.1
> ? 0.00 0.0 0.30 55.6
> eval 0.00 0.0 0.30 55.6
> FUN 0.00 0.0 0.30 55.6
> help 0.00 0.0 0.30 55.6
> lapply 0.00 0.0 0.30 55.6
> sapply 0.00 0.0 0.30 55.6
> print 0.00 0.0 0.24 44.4
> print.help_files_with_topic 0.00 0.0 0.24 44.4
> dyn.load 0.00 0.0 0.06 11.1
>
> $by.total
> total.time total.pct self.time self.pct
> index.search 0.30 55.6 0.30 55.6
> ? 0.30 55.6 0.00 0.0
> eval 0.30 55.6 0.00 0.0
> FUN 0.30 55.6 0.00 0.0
> help 0.30 55.6 0.00 0.0
> lapply 0.30 55.6 0.00 0.0
> sapply 0.30 55.6 0.00 0.0
> print 0.24 44.4 0.00 0.0
> print.help_files_with_topic 0.24 44.4 0.00 0.0
> .C 0.18 33.3 0.18 33.3
> inDL 0.06 11.1 0.06 11.1
> dyn.load 0.06 11.1 0.00 0.0
>
> $sampling.time
> [1] 0.54
>
>
>
> On Tue, Nov 4, 2008 at 12:53 PM, Gabor Grothendieck
> <ggrothendieck_at_gmail.com> wrote:
>> Are you sure?
>>
>> summaryRprof()
>>
>> says that based on your Rprof.out file that 55% of the time is being spent
>> in index.search which is for searching help files.
>>
>>
>> On Tue, Nov 4, 2008 at 12:36 PM, stephen sefick <ssefick_at_gmail.com> wrote:
>>> this is from the read.production command
>>>
>>> On Tue, Nov 4, 2008 at 12:09 PM, Gabor Grothendieck
>>> <ggrothendieck_at_gmail.com> wrote:
>>>> See ?Rprof
>>>>
>>>> On Tue, Nov 4, 2008 at 12:01 PM, stephen sefick <ssefick_at_gmail.com> wrote:
>>>>> R version 2.8.0 (2008-10-20)
>>>>> i386-pc-mingw32
>>>>>
>>>>> locale:
>>>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>>>> States.1252;LC_MONETARY=English_United
>>>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] StreamMetabolism_0.01 chron_2.3-24 zoo_1.5-4
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] grid_2.8.0 lattice_0.17-15
>>>>>
>>>>>
>>>>> I have a large data set that I have been reading in the same way
>>>>> read.production() from the StreamMetabolism package and it has worked
>>>>> in the past without a hitch
>>>>>
>>>>> ##########code provided#############
>>>>> read.production <- function(data) { read.zoo(data, sep = ",", FUN =
>>>>> fmt.chron, header = TRUE)}
>>>>>
>>>>> fmt.chron <- function (x) {chron(sub(" .*", "", x), gsub(".* (.*)",
>>>>> "\\1:00", x))}
>>>>>
>>>>> this is the first time that I have used this data since the upgrade to
>>>>> 2.8 and it is taking longer to preform operations. What can I do to
>>>>> help diagnose the problem. I know this is not reproducible, but I
>>>>> don't know without sharing the entire data set how to do that.
>>>>> Thanks in advance
>>>>>
>>>>>
>>>>> --
>>>>> Stephen Sefick
>>>>> Research Scientist
>>>>> Southeastern Natural Sciences Academy
>>>>>
>>>>> Let's not spend our time and resources thinking about things that are
>>>>> so little or so large that all they really do for us is puff us up and
>>>>> make us feel like gods. We are mammals, and have not exhausted the
>>>>> annoying little problems of being mammals.
>>>>>
>>>>> -K. Mullis
>>>>>
>>>>> ______________________________________________
>>>>> R-help_at_r-project.org mailing list
>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> Stephen Sefick
>>> Research Scientist
>>> Southeastern Natural Sciences Academy
>>>
>>> Let's not spend our time and resources thinking about things that are
>>> so little or so large that all they really do for us is puff us up and
>>> make us feel like gods. We are mammals, and have not exhausted the
>>> annoying little problems of being mammals.
>>>
>>> -K. Mullis
>>>
>>
>

-- 
Stephen Sefick
Research Scientist
Southeastern Natural Sciences Academy

Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods.  We are mammals, and have not exhausted the
annoying little problems of being mammals.

								-K. Mullis

______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Received on Tue 04 Nov 2008 - 18:12:54 GMT

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