[R] Zoo seems to be running slow in R 2.8.0 windows
Gabor Grothendieck
ggrothendieck at gmail.com
Tue Nov 4 19:37:01 CET 2008
On Tue, Nov 4, 2008 at 1:06 PM, stephen sefick <ssefick at gmail.com> wrote:
> 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
It indicates that chron's [.times is where a lot of time is being spent.
Try reading in the data using POSIXct rather than chron/times and see
if you get a speedup. Specify tz= and format= in read.zoo in order to do that.
The percent codes for format= are in ?strptime . You can issue the
R command:
Sys.setenv(TZ = "GMT")
first to avoid time zone problems.
> results? Or do you want it copy and pasted into the email?
> thank you very much
attaching Rprof.out and pasting the output of summaryRprof() into your
mail message should be adequate.
>
> 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
>
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