problems running ChromosomeExplorer with linux
lixia diao
glad <- GladModel(cesNlist)
fit(glad, arrays=c(1,8),chromosomes=c(19,22),verbose=TRUE)
ce <- ChromosomeExplorer(glad)
When I run the last command line, all linux windows closes. I am not sure why it happens that I can't process it.
Thanks a lot,
Henrik Bengtsson
On Tue, Jul 8, 2008 at 10:30 AM, lixia diao <dia...@gmail.com> wrote:
> Hi,
>
> I am using aroma.affymetrix to analyze Affymetrix 250K SNP Sty file. I used
> linux system. R version is 2.7.0, aroma.affymetrix_0.9.3.
Please report your complete sessionInfo().
> I tried to
> utilize ChromosomeExplorer class to fit the model and to generate browsable
> image files. The code looks like:
> glad <- GladModel(cesNlist)
> fit(glad, arrays=c(1,8),chromosomes=c(19,22),verbose=TRUE)
>
> ce <- ChromosomeExplorer(glad)
>
> When I run the last command line, all linux windows closes. I am not sure
> why it happens that I can't process it.
I cannot see how calling:
ce <- ChromosomeExplorer(glad)
will "crash" (or whatever happens) your R session. There is nothing
extrodinary happening when that is called. Does it really "crash"
there or when you call something else?
You have to be more specific, e.g. does it crash all applications
running on your Linux machine, just R, does it only close the open R
figure windows, can you do anything in R afterwards and so. Can you
do traceback()? What does it tell you?
/Henrik
>
> Thanks a lot,
>
> >
>
lixia
The sesionInfo looks:
> sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_attached
base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GLAD_1.16.0 aroma.affymetrix_0.9.3 aroma.apd_0.1.3
[4] R.huge_0.1.5 EBImage_2.4.0 affxparser_1.12.2
[7] aroma.core_0.9.3 sfit_0.1.5 aroma.light_1.8.1
[10] digest_0.3.1 matrixStats_0.1.2 R.rsp_0.3.4
[13] R.cache_0.1.7 R.utils_1.0.2 R.oo_1.4.3
[16] R.methodsS3_1.0.1 xtable_1.5-2
loaded via a namespace (and not attached):
[1] RColorBrewer_1.0-2 tools_2.7.0
Because I only run R using the Linux server at that time, when I
process the command line, it closes R figure window and the linux
command window. So I have to log in to the linux server again.
Thanks,
Lixia
does it crash all applications
> running on your Linux machine, just R, does it only close the open R
> figure windows, can you do anything in R afterwards and so. Can you
> do traceback()? What does it tell you?
>
> - Show quoted text -
Henrik Bengtsson
On Tue, Jul 8, 2008 at 11:53 AM, lixia <dia...@gmail.com> wrote:
>
> Hi,
>
> The sesionInfo looks:
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> i686-pc-linux-gnu
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_attached
> base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] GLAD_1.16.0 aroma.affymetrix_0.9.3 aroma.apd_0.1.3
> [4] R.huge_0.1.5 EBImage_2.4.0 affxparser_1.12.2
> [7] aroma.core_0.9.3 sfit_0.1.5 aroma.light_1.8.1
> [10] digest_0.3.1 matrixStats_0.1.2 R.rsp_0.3.4
> [13] R.cache_0.1.7 R.utils_1.0.2 R.oo_1.4.3
> [16] R.methodsS3_1.0.1 xtable_1.5-2
> loaded via a namespace (and not attached):
> [1] RColorBrewer_1.0-2 tools_2.7.0
>
> Because I only run R using the Linux server at that time, when I
> process the command line, it closes R figure window and the linux
> command window. So I have to log in to the linux server again.
This sound like it crashes R, but it would be good if you really good
check that with your sysadm. Basically, does it "core dump" the
running R process? That is extremely important to know for
troubleshooting. If it only "quits" (SIG-INT or similar; your sysadm
should know what this is), then something else happens.
Also can you please confirm that it indeed crashes when you call:
ce <- ChromosomeExplorer(glad);
and not before and not after. This is very important to know for the
troubleshooting.
/Henrik
lixia
I am sure that it crashes when I call ce <- ChromosomeExplorer(glad),
not before or after. I am not sure what you mean "core dump" the
running R process. But I will talk to some sysadm first and if they
also can't solve this problem, I will let you know.
Thank you so much for the help,
Lixia
Henrik Bengtsson
On Tue, Jul 8, 2008 at 1:04 PM, lixia <dia...@gmail.com> wrote:
>
> Hi,
>
> I am sure that it crashes when I call ce <- ChromosomeExplorer(glad),
> not before or after.
You can then use
debug(ChromosomeExplorer)
debug(Explorer)
debug(Object)
before call it. That will allow you to step through inside these
functions and narrow down where it goes wrong. However, I still
cannot see anything in those constructor functions that
could cause R to crash.
/Henrik
lixia
Thanks a lot for the instruction. I talked to the sysadm, they tried
some ways to let the ChromosomeExplorer, process steps run. I can get
the ChromosomeExplorer.html open manually. But when I tried to use
display(ce) after the ChromosomeExplorer and process steps, it will
give some memory warning messages, and although the firefox window
opens, it shows "File not found". I checked the path the file shows,
it seems to duplicate the path, which means: I run the program under
some folder home/SNP/practice, then the file path on the firefox
window show home/SNP/practice\home\SNP\practice\reports\.....
\ChromosomeExplorer.html. I am guessing it is because I didn't run it
at the rooter directory or the program should be run under some rooter
directory.
Henrik Bengtsson
I suggest that you follow the instructions in the vignettes *exactly*
as is. Do not deviate for instance by working in separate directories
etc. Try it on a small data set to see how it should work.
If you have any further problems, post *verbatim* error, warning, and
verbose output you see. For troubleshooting purposes, please don't
rewrite them in your own words.
Cheers
/Henrik