[R] chron and R 2.8
Gabor Grothendieck
ggrothendieck at gmail.com
Mon Dec 1 19:32:39 CET 2008
Please provide the input file so its reproducible.
On Mon, Dec 1, 2008 at 1:12 PM, stephen sefick <ssefick at gmail.com> wrote:
> These are the two functions that I use to read the data in. I have
> reverted back to R 2.7.2, chron 2.3-24, zoo 1.5-4, StreamMetabolism
> 0.03. This configuration works just fine- like I expect and with
> considerable time speed up over both R 2.8 and chron 2.3-24 and
> 2.3-25.
>
> fmt.chron <- function (x)
> {
> chron(sub(" .*", "", x), gsub(".* (.*)", "\\1:00", x))
> }
>
> read.production <- function (data)
> {
> read.zoo(data, sep = ",", FUN = fmt.chron, header = TRUE)
> }
>
>
> DateTime RM215Temp
> 800 1/9/06 7:46 11.12
> 801 1/9/06 8:01 11.11
> 802 1/9/06 8:16 10.98
> 803 1/9/06 8:31 10.90
> 804 1/9/06 8:46 10.94
> 805 1/9/06 9:01 10.98
> 806 1/9/06 9:16 10.98
> 807 1/9/06 9:31 11.00
> 808 1/9/06 9:46 11.02
> 809 1/9/06 10:01 11.04
> 810 1/9/06 10:16 11.06
> 811 1/9/06 10:31 11.07
> 812 1/9/06 10:46 11.09
> 813 1/9/06 11:01 11.11
> 814 1/9/06 11:16 11.13
> 815 1/9/06 11:31 11.16
> 816 1/9/06 11:46 11.18
> 817 1/9/06 12:01 11.20
> 818 1/9/06 12:16 11.23
> 819 1/9/06 12:31 11.27
> 820 1/9/06 12:46 11.30
> 821 1/9/06 13:01 11.33
> 822 1/9/06 13:16 11.36
> 823 1/9/06 13:31 11.39
> 824 1/9/06 13:46 11.42
> 825 1/9/06 14:01 11.44
> 826 1/9/06 14:16 11.45
> 827 1/9/06 14:31 11.48
> 828 1/9/06 14:46 11.50
> 829 1/9/06 15:01 11.52
> 830 1/9/06 15:16 11.54
> 831 1/9/06 15:31 11.56
> 832 1/9/06 15:46 11.59
> 833 1/9/06 16:01 11.61
> 834 1/9/06 16:16 11.64
> 835 1/9/06 16:31 11.64
> 836 1/9/06 16:46 11.64
> 837 1/9/06 17:01 11.62
> 838 1/9/06 17:16 11.60
> 839 1/9/06 17:31 11.58
> 840 1/9/06 17:46 11.57
> 841 1/9/06 18:01 11.60
> 842 1/9/06 18:16 11.57
> 843 1/9/06 18:31 11.45
> 844 1/9/06 18:46 11.40
> 845 1/9/06 19:01 11.44
> 846 1/9/06 19:16 11.38
> 847 1/9/06 19:31 11.39
> 848 1/9/06 19:46 11.43
> 849 1/9/06 20:01 11.40
> 850 1/9/06 20:16 11.44
> 851 1/9/06 20:31 11.24
> 852 1/9/06 20:46 11.08
> 853 1/9/06 21:01 11.10
> 854 1/9/06 21:16 11.08
> 855 1/9/06 21:31 11.08
> 856 1/9/06 21:46 11.08
> 857 1/9/06 22:01 11.07
> 858 1/9/06 22:16 11.07
> 859 1/9/06 22:31 11.08
> 860 1/9/06 22:46 11.08
> 861 1/9/06 23:01 11.07
> 862 1/9/06 23:16 11.07
> 863 1/9/06 23:31 11.06
> 864 1/9/06 23:46 11.06
> 865 1/10/06 0:01 11.05
> 866 1/10/06 0:16 11.05
> 867 1/10/06 0:31 11.05
> 868 1/10/06 0:46 11.04
> 869 1/10/06 1:01 11.04
> 870 1/10/06 1:16 11.03
> 871 1/10/06 1:31 11.03
> 872 1/10/06 1:46 11.02
> 873 1/10/06 2:01 11.02
> 874 1/10/06 2:16 11.01
> 875 1/10/06 2:31 11.01
> 876 1/10/06 2:46 11.01
> 877 1/10/06 3:01 11.00
> 878 1/10/06 3:16 10.99
> 879 1/10/06 3:31 10.99
> 880 1/10/06 3:46 10.99
> 881 1/10/06 4:01 10.98
> 882 1/10/06 4:16 10.97
> 883 1/10/06 4:31 10.97
> 884 1/10/06 4:46 10.96
> 885 1/10/06 5:01 10.95
> 886 1/10/06 5:16 10.95
> 887 1/10/06 5:31 10.94
> 888 1/10/06 5:46 10.93
> 889 1/10/06 6:01 10.93
> 890 1/10/06 6:16 10.93
> 891 1/10/06 6:31 10.94
> 892 1/10/06 6:46 10.93
> 893 1/10/06 7:01 10.90
> 894 1/10/06 7:16 10.90
> 895 1/10/06 7:31 10.91
> 896 1/10/06 7:46 10.92
>
>
> On Mon, Dec 1, 2008 at 12:08 PM, Gabor Grothendieck
> <ggrothendieck at gmail.com> wrote:
>> The key thing to do is to provide some reproducible code that
>> someone else can use to verify the problem even if you have
>> to use it on 2.7.2 with the old chron and 2.8.0 with the new chron.
>>
>>
>> On Mon, Dec 1, 2008 at 11:34 AM, stephen sefick <ssefick at gmail.com> wrote:
>>> I have built chron 2.3-24 under 2.8 and it is acting the same as
>>> 2.3-24 and as to the previous email the zoo version is the same for
>>> both. My next test will be to get 2.7.2 up and running again, and see
>>> what the behavior is under this version with the different versions of
>>> chron. I have not figured out how to install || versions of R in mac
>>> OS X it looks like the packages are maintained but the application is
>>> automatically removed and updated into the current version. What else
>>> should I try?
>>>
>>> On Mon, Dec 1, 2008 at 10:41 AM, Gabor Grothendieck
>>> <ggrothendieck at gmail.com> wrote:
>>>> Two things to try:
>>>>
>>>> - try running both under 2.7.2 instead of trying both under 2.8
>>>> - if you know how to build packages from source then try rebuilding the
>>>> chron you have under 2.7.2 using 2.98. You can find it here:
>>>> http://cran.r-project.org/src/contrib/Archive/chron/
>>>>
>>>>
>>>> On Mon, Dec 1, 2008 at 10:35 AM, stephen sefick <ssefick at gmail.com> wrote:
>>>>> I found the library where all of the older packages are located.
>>>>>
>>>>> library(chron, lib =
>>>>> "/Library/Frameworks/R.Framework/Versions/2.7/Resources/library")
>>>>>
>>>>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>>>> unable to load shared library
>>>>> '/Library/Frameworks/R.Framework/Versions/2.7/Resources/library/chron/libs/i386/chron.so':
>>>>> dlopen(/Library/Frameworks/R.Framework/Versions/2.7/Resources/library/chron/libs/i386/chron.so,
>>>>> 6): Library not loaded:
>>>>> /Library/Frameworks/R.framework/Versions/2.7/Resources/lib/libR.dylib
>>>>> Referenced from:
>>>>> /Library/Frameworks/R.Framework/Versions/2.7/Resources/library/chron/libs/i386/chron.so
>>>>> Reason: image not found
>>>>> Error: package/namespace load failed for 'chron'
>>>>>
>>>>> The code above works with zoo
>>>>> library(zoo, lib =
>>>>> "/Library/Frameworks/R.Framework/Versions/2.7/Resources/library")
>>>>>
>>>>>
>>>>> On Sun, Nov 30, 2008 at 10:04 PM, Gabor Grothendieck
>>>>> <ggrothendieck at gmail.com> wrote:
>>>>>> To run the old version of chron that you have under 2.7.2
>>>>>> into 2.8.0, on 2.7.2 issue the command (note initial dot):
>>>>>>
>>>>>> .libPaths()
>>>>>>
>>>>>> Suppose you find that the library that contains chron in
>>>>>> 2.7.2 is "/a/b".
>>>>>>
>>>>>> Then on 2.8.0 ensure that you don't have chron on the search path
>>>>>>
>>>>>> search()
>>>>>>
>>>>>> and if you do detach it:
>>>>>>
>>>>>> detach("package:chron")
>>>>>> search() # should no longer be there
>>>>>>
>>>>>> Then run this where "..." is the library that the old version of chron
>>>>>> is in under 2.7.2.
>>>>>>
>>>>>> library(chron, lib = "...")
>>>>>>
>>>>>> To run the new version of chron detach the old version and just use:
>>>>>>
>>>>>> library(chron)
>>>>>>
>>>>>>
>>>>>> On Sun, Nov 30, 2008 at 9:14 PM, stephen sefick <ssefick at gmail.com> wrote:
>>>>>>> Yes
>>>>>>> chron 2.3-25
>>>>>>> zoo 1.5-4
>>>>>>> R 2.8
>>>>>>> Mac OS X 10.5.5
>>>>>>>
>>>>>>> Gabor I don't know how to start up another verison of R on the mac. I
>>>>>>> will figure this out, and get back to you (I can then test both of
>>>>>>> them side by side).
>>>>>>>
>>>>>>> other fast installation (version numbers from description files in R
>>>>>>> 2.7.2 directory)
>>>>>>> chron 2.3-24
>>>>>>> zoo 1.5-4
>>>>>>> Mac OS X 10.5.5
>>>>>>>
>>>>>>> thanks
>>>>>>>
>>>>>>> Stephen
>>>>>>>
>>>>>>> On Sat, Nov 29, 2008 at 10:19 AM, Gabor Grothendieck
>>>>>>> <ggrothendieck at gmail.com> wrote:
>>>>>>>> Are you using the same version of chron both times?
>>>>>>>>
>>>>>>>> On Sat, Nov 29, 2008 at 10:05 AM, stephen sefick <ssefick at gmail.com> wrote:
>>>>>>>>> has anyone had problems with the upgrade to R 2.8 and chron date
>>>>>>>>> classes. I have a large zoo object that has a chron index, and it is
>>>>>>>>> taking 5x or so longer to do the same calculation as with 2.7 if it
>>>>>>>>> doesn't fail. I will provide anything necessary I am not entirely
>>>>>>>>> sure what ya'll would need if anything to try and reproduce the
>>>>>>>>> behavior. I am using the package StreamMetabolism.
>>>>>>>>> thanks
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Stephen Sefick
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>
>>>>>>> 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
>>>>>
>>>>> 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
>>>
>>> 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
>
> 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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