[R] Zoo seems to be running slow in R 2.8.0 windows
Gabor Grothendieck
ggrothendieck at gmail.com
Tue Nov 4 19:43:25 CET 2008
One other question. Are you running the same version of the chron
package on both 2.7.2 and 2.8.0?
packageDescription("chron")$Version
will tell you. If there is a version difference does changing the
chron version change the performance?
On Tue, Nov 4, 2008 at 1:37 PM, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> 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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