[vtkusers] can not find some function of R when use R integrated in vtk

[Wes Turner]

That looks reasonable.  When you do:

ls
/home/lwen/development/StandAloneBRAINSSurfaceStats_build/R-build/library/

is the correct shared library displayed?

- Wes

On Tue, Mar 1, 2011 at 12:17 PM, Li, Wen <wen-li at uiowa.edu> wrote:

> Wes,
>
>
>
> It did not work for me.
>
>
>
> Just want to make sure I did the right thing.
>
>
>
> Before running my program, I did
>
> export
> "LD_LIBRARY_PATH=/home/lwen/development/StandAloneBRAINSSurfaceStats_build/R-buil
>
> d/library/:$LD_LIBRARY_PATH"
>
>
>
> echo $LD_LIBRARY_PATH
>
> it shows:
>
>
> /home/lwen/development/StandAloneBRAINSSurfaceStats_build/R-build/library/:/usr/
>
> lib64/mpi/gcc/openmpi/lib64
>
>
>
> Then I ran my program. Still got the errors and cannot find the function.
>
>
>
> Wen
>
>
>
> *From:* Wes Turner [mailto:wes.turner at kitware.com]
> *Sent:* Tuesday, March 01, 2011 9:57 AM
>
> *To:* Li, Wen
> *Cc:* vtkusers at vtk.org
> *Subject:* Re: [vtkusers] can not find some function of R when use R
> integrated in vtk
>
>
>
> I believe that you can (I have multiple R installations on my windows box
> and it works).  Setting it up is slightly different than on Linux (I only
> have one R installed on Linux).  I believe the first library encountered in
> LD_LIBRARY_PATH is the one that gets used preferentially, so if you do
> something like export
> "LD_LIBRARY_PATH=preferred_R_installation:$LD_LIBRARY_PATH" it *should*
> work.
>
>
>
> - Wes
>
> On Tue, Mar 1, 2011 at 10:29 AM, Li, Wen <wen-li at uiowa.edu> wrote:
>
> Wes,
>
>
>
> I agree. We know that R_HOME is set to be correct so we can do lib path in
> the same way?
>
>
>
> Just my 2 centsJ
>
>
>
> BTW: We tested our vtk program with R on a Linux machine.
>
>
>
> Thanks,
>
> Wen
>
>
>
>
>
> *From:* Wes Turner [mailto:wes.turner at kitware.com]
> *Sent:* Tuesday, March 01, 2011 7:48 AM
>
>
> *To:* Li, Wen
> *Cc:* vtkusers at vtk.org
> *Subject:* Re: [vtkusers] can not find some function of R when use R
> integrated in vtk
>
>
>
> Wen Li,
>
>
>
> Thanks for sending this back.  This is undoubtedly something that we will
> have to understand better as we move forward.  I would expect that it is
> mainly a matter of cleaning up the environment and setting paths/shared
> libraries correctly.  Is your machine a windows box, or Linux, or Mac, or
> ...?  The easiest trick we have found so far, is simply to include the
> correct R libraries in the directory with the executable.  That is the first
> place that should be searched.  I will post if we get a better solution.
>
>
>
> - Wes
>
> On Tue, Mar 1, 2011 at 8:39 AM, Li, Wen <wen-li at uiowa.edu> wrote:
>
> Wes,
>
>
>
> R_HOME was set correctly.
>
>
>
> We found out the reason but we don’t have a very good solution so far.
>
>
>
> It is because we have multiple versions of R installed in the operating
> system.
>
> When we ran R by vtk, it had trouble finding the correct lib path.
>
>
>
> Now we are simply running it on a clean operating system and we don’t
>
> see the errors and any problem using functions like read.csv().
>
>
>
> It will be very nice if someone can give a better solution.
>
>
>
> Best,
>
> Wen Li
>
>
>
> *From:* Wes Turner [mailto:wes.turner at kitware.com]
> *Sent:* Monday, February 28, 2011 8:53 AM
> *To:* Li, Wen
> *Cc:* vtkusers at vtk.org
> *Subject:* Re: [vtkusers] can not find some function of R when use R
> integrated in vtk
>
>
>
> Do you have the R_HOME variable set to the results of executing "R RHOME"?
>
> - Wes
>
>
>
> On Fri, Feb 25, 2011 at 4:49 PM, Li, Wen <wen-li at uiowa.edu> wrote:
>
> Hi, all
>
>
>
> We have been trying to use R in vtk to do some statistic analysis for
> surfaces.
>
>
>
> The program was running perfectly when we simply used functions like “mean”
> and “sum” in our R script.
>
>
>
> But when we try to use other functions like “read.csv()”, it complains that
> this function can not be found.
>
>
>
> And we see the errors like,
>
>
>
>
> --------------------------------------------------------------------------------------------
>
> Error in identical(env, as.environment(i)) :
>
>   5 arguments passed to .Internal(identical) which requires 2
>
> Error in file(paste(tempdir(), "/Routput.txt", sep = ""), open = "wt+") :
>
>   5 arguments passed to .Internal(file) which requires 4
>
> Error in identical(arg, choices) :
>
>   5 arguments passed to .Internal(identical) which requires 2
>
>
> -----------------------------------------------------------------------------------------------
>
>
>
> Any help or suggestion to solve this problem will be appreciated.
>
>
>
> Thank you in advance.
>
>
>
> Wen Li
>
> The University of Iowa
>
>
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>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>
>
>
>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>
>
>
>
> --
> Wesley D. Turner, Ph.D.
> Kitware, Inc.
> Technical Leader
> 28 Corporate Drive
> Clifton Park, NY 12065-8662
> Phone: 518-881-4920
>



-- 
Wesley D. Turner, Ph.D.
Kitware, Inc.
Technical Leader
28 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4920
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