[R] Objects disappearing in my R work space

Sat Nov 26 01:59:32 CET 2011

at least put

print(str(Samples))

right after the function call to make sure it is there, and if you
have more code after that, sprinkle that print statement in the
following code.  You might at least send the code and indicate where
you have tested to see if the object is still there.

So put some of those print statements to help isolate what section of
code the problem is happening in  because just saying it disappears is
not sufficient.  This is elementary debugging of a program.  If your
program is as big and complicated as you say, then you have to start
learning some debugging techniques to help you find where the problem
is.

On Fri, Nov 25, 2011 at 7:48 PM, Michael Clawson
<michael.v.clawson at gmail.com> wrote:
> I am returning a matrix from a function
> Samples<-DoMCMC(InitialVactor, CovarianceMatrix, ObservationData, NumCycles,
> Burnin, Thin)
> When I have one R session open the program works, Samples is a matrix of
> samples from the MCMC
> When I have two R sessions open, it runs to completion, but when I got to
> view Samples, it is not there.
> by disappear, I mean I define Samples as above, and when it finishes cycling
> through
> I type Samples and it says it doesn't exist, I type the command: ls() and it
> is not in the list of objects defined in the session.
> How would something I am doing in the code be affected by how many R
> sessions are open? I have tried this on two different machines, one running
> Windows XP and one Windows 7. but both running R 2.13.1
> Thank you all for all of the responses, sorry if my inexperience in R is
> hindering this process
>
> On Fri, Nov 25, 2011 at 4:06 PM, jim holtman <jholtman at gmail.com> wrote:
>>
>> One thing is to define "missing" a little better.  For example, as
>> mentioned previously, are you returning the values from a function
>> call?  If you, print out an indication that they exist at that point.
>> If there is further processing happening, put some checks as to their
>> existance as the code continues.  Can you localize where this is
>> happening?  If they are "disappearing", then there is something you
>> are doing in your code to most likely make it happen.  Until there is
>> something that people can reproduce, there are all types of theories
>> we can expound on.
>>
>> If I was looking at the code, I could probably put checks in at
>> various points to see in what section these things disappeared.  Do
>> you have some 'try' functions around parts of the code that might not
>> be reporting some error conditions?  So probably until you can provide
>> something that we can at least look at, and exactly how you determined
>> that something disappeared, there is probably not much more we can do
>> at this point.
>>
>> On Fri, Nov 25, 2011 at 6:19 PM, Duncan Murdoch
>> <murdoch.duncan at gmail.com> wrote:
>> > On 11-11-25 1:03 PM, Michael Clawson wrote:
>> >>
>> >> My problem with providing the code, is MCMC is a fairly integrated
>> >> process,
>> >> so I dont know how I would pare it down to send...
>> >> Would it work to send the MCMC code, and the three *.csv files to go
>> >> along
>> >> with it?
>> >
>> > I don't understand.  If you can't make your code simple enough to post,
>> > how
>> > do you think we can possibly imagine what you're doing?
>> >
>> > Duncan Murdoch
>> >
>> >>
>> >> On Fri, Nov 25, 2011 at 9:54 AM, David
>> >> Winsemius<dwinsemius at comcast.net>wrote:
>> >>
>> >>>
>> >>> On Nov 25, 2011, at 10:08 AM, Michael Clawson wrote:
>> >>>
>> >>>  Uwe,
>> >>>>
>> >>>> by window I mean instances, by runs I mean, runs the my Markov-Chain
>> >>>> Monte
>> >>>> Carlo simulator
>> >>>>
>> >>>
>> >>> It would probably be better to adopt the terminology that the things
>> >>> you
>> >>> are calling "windows" are "sessions".
>> >>>
>> >>>
>> >>>> I open two instances of R, run a million cycle chain in each
>> >>>> instance,
>> >>>> and
>> >>>> when they finish, neither window has the object I defined to store
>> >>>> the
>> >>>> runs.
>> >>>>
>> >>>> I tested this morning and when I open two R windows and run a 5k
>> >>>> cycle
>> >>>> chain in each instance, neither window has the object I defined to
>> >>>> store
>> >>>> the runs.
>> >>>>
>> >>>> This does not happen when I only have one instance of R open
>> >>>>
>> >>>
>> >>> The most common cause of that behavior is failing to assign the output
>> >>> of
>> >>> a function to a name. There is an object named ".Last.value" that
>> >>> hosld
>> >>> the
>> >>> results of the last returned object even it it doesn't have another
>> >>> name.
>> >>>
>> >>> lapply(1:10,  I)
>> >>> test<- .Last.value
>> >>> test
>> >>> [[1]]
>> >>> [1] 1
>> >>>
>> >>> [[2]]
>> >>> [1] 2
>> >>> snipped rest of output
>> >>>
>> >>> But as Uwe said ... without the code, ... and your OS (to answer the
>> >>> question about memory)  .... and your sessionInfo() to make sure that
>> >>> this
>> >>> is not a GUI-related issue ... we cannot say very much.
>> >>>
>> >>>
>> >>>
>> >>>
>> >>>> 2011/11/25 Uwe
>> >>>>
>> >>>> Ligges<ligges at statistik.tu-dortmund.**de<ligges at statistik.tu-dortmund.de>
>> >>>>>
>> >>>>
>> >>>>
>> >>>>>
>> >>>>> On 25.11.2011 05:12, Aldo wrote:
>> >>>>>
>> >>>>>  Is there a maximum memory allocation for all R windows open?
>> >>>>> because
>> >>>>> it
>> >>>>>>
>> >>>>>> is
>> >>>>>> like 1-3 million runs
>> >>>>>>
>> >>>>>>
>> >>>>> ????
>> >>>>> So you mean you open a million windows at the same time? In that
>> >>>>> case
>> >>>>> we
>> >>>>> really need your definition of "window".
>> >>>>>
>> >>>>>
>> >>>>> .... so... it may be reaching some sort of memory limit
>> >>>>>
>> >>>>>>
>> >>>>>>
>> >>>>> I do not know if any OS / window manager has the capability to open
>> >>>>> that
>> >>>>> many numbers of windows. But as I said, we need some difintions and
>> >>>>> examples.
>> >>>>>
>> >>>>> Uwe Ligges
>> >>>>>
>> >>>>> --
>> >>>>>
>> >>>>
>> >>> David Winsemius, MD
>> >>> West Hartford, CT
>> >>>
>> >>>
>> >>
>> >>        [[alternative HTML version deleted]]
>> >>
>> >> ______________________________________________
>> >> 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.
>> >
>> > ______________________________________________
>> > 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.
>> >
>>
>>
>>
>> --
>> Jim Holtman
>> Data Munger Guru
>>
>> What is the problem that you are trying to solve?
>> Tell me what you want to do, not how you want to do it.
>
>

-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.