On Mon, Nov 15, 2010 at 9:55 PM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
> Hi
>
> I did install it as suggested.
Ok, so you still get that message? Then try to uninstall the dummy
EBImage by first doing:
remove.packages("EBImage");
and assert that it is truly removed by calling library("EBImage") -
you should get an error.
Then restart R, and try to install from Bioconductor.
/Henrik
> But again as mentioned it could be due to the version of R. we are
> trying to get R updated and will see how things go from there.
>
> Thanks for the assistance
> Regards
> Elsa
>
> On Nov 16, 4:45 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> I see, so you found a dummy version of EBImage over at R-forge. Now
>> it make sense. That is *not* the version you wish to install (the
>> message explains why that dummy version exists in the first place).
>> Instead, go to Bioconductor and install it. Something like:
>>
>> source("http://bioconductor.org/biocLite.R";);
>> biocLite("EBImage");
>>
>> As I said before, you may want/need to update your version of R.
>>
>> /Henrik
>>
>> On Mon, Nov 15, 2010 at 9:37 PM, Elsa Chacko <elsa.cha...@gmail.com> wrote:
>> > Hi
>>
>> > Sorry I should have posted the error i got :
>>
>> > Loaded EBImage v9.9.9 (2009-09-10). HOWEVER, DO NOT INSTALL THIS
>> > PACKAGE. THIS IS AN EMPTY PACKAGE WITH THE SAME NAME AS AN EXISTING
>> > BIOC PACKAGE. THE ONLY PURPOSE OF THIS PACKAGE IS TO PREVENT THE R-
>> > FORGE BUILD SERVERS TO HALT THE BUILDING OF AROMA.CORE AND
>> > AROMA.AFFYMETRIX. THIS DUMMY PACKAGE WILL NOT BE NEEDED WHEN R-FORGE
>> > INCLUDES THE REAL EBIMAGE PACKAGE OR SETS
>> > R_check_force_suggests=false.
>>
>> > Seeing the aroma.affymetrix in the message i wrongly assumed that this
>> > is an error message from the aroma package..
>>
>> > Thanks for the assistance
>> > Regards
>> > Elsa
>>
>> > On Nov 16, 4:18 pm, Henrik Bengtsson <henrik.bengts...@aroma-
>> > project.org> wrote:
>> >> Hi.
>>
>> >> On Mon, Nov 15, 2010 at 8:50 PM, Elsa Chacko <elsa.cha...@gmail.com>
>> >> wrote:
>> >> > Hi
>>
>> >> > I am trying to implement the Vignette: Human exon array analysis
>> >> > posted athttp://www.aroma-project.org/node/37.
>>
>> >> > However when i got to the section discussing how to browse spatial
>> >> > false-colored images of the residuals,
>>
>> >> > ae <- ArrayExplorer(rs)
>> >> > setColorMaps(ae, c("log2,log2neg,rainbow", "log2,log2pos,rainbow"))
>> >> > process(ae, interleaved="auto", verbose=verbose)
>>
>> >> > i got the error the EBImage package not loaded.
>>
>> >> > So i went and installed the EBImage package from bioconductors and now
>> >> > i get an error stating that i should not have installed this package.
>>
>> >> Where does it say you "should not have installed [the EBImage]
>> >> package"? I am not sure I understand.
>>
>> >> > Any help resolving this is very much appreciated?
>>
>> >> Whatever the error EBImage reports, I believe it is independent of the
>> >> aroma.affymetrix et al. packages. Because of this, I recommend that
>> >> you troubleshoot this without loading aroma.affymetrix, but instead
>> >> start a fresh R session and make sure you can load EBImage, e.g.
>>
>> >> % R --vanilla
>> >> [...]
>>
>> >> > library("EBImage");
>>
>> >> without errors (warnings are ok). If you get errors here, please ask
>> >> for further assistance on the Bioconductor mailing list
>> >> [http://bioconductor.org/help/mailing-list/], because that is the
>> >> place to find people that can help you with EBImage and other
>> >> Bioconductor packages.
>>
>> >> Also, it may be that there is not compatible version of EBImage for
>> >> your OS/platform. The Bioc experts will let you know if this is the
>> >> case.
>>
>> >> >> sessionInfo()
>> >> > R version 2.10.1 (2009-12-14)
>>
>> >> Your installation of R is nearly one year old and considered obsolete;
>> >> I recommend that you also update R to the latest R 2.12.0 (preferably
>> >> the patched version). Over at Bioconductor, they'll most likely ask
>> >> you to do that.
>>
>> >> Hope this helps
>>
>> >> /Henrik
>>
>> >> > x86_64-pc-linux-gnu
>>
>> >> > locale:
>> >> > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
>> >> > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
>> >> > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8
>> >> > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
>> >> > [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >> > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> >> > attached base packages:
>> >> > [1] stats graphics grDevices utils datasets methods base
>>
>> >> > loaded via a namespace (and not attached):
>> >> > [1] tools_2.10.1
>>
>> >> >> traceback()
>> >> > 3: stop(gettextf("no methods for '%s' and no documentation for it as a
>> >> > function",
>> >> > f), domain = NA)
>> >> > 2: .helpForCall(topicExpr, parent.frame())
>> >> > 1: `?`(EBImage())
>>
>> >> > Regards
>> >> > Elsa Chacko
>> >> > PhD Student
>> >> > Macquarie University.
>>
>> >> > --
>> >> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> > latest version of the package, 2) to report the output of sessionInfo()
>> >> > and
>> >> > traceback(), and 3) to post a complete code example.
>>
>> >> > You received this message because you are subscribed to the Google
>> >> > Groups "aroma.affymetrix" group with
>> >> > websitehttp://www.aroma-project.org/.
>> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> >> > To unsubscribe and other options, go
>> >> > tohttp://www.aroma-project.org/forum/
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> > version of the package, 2) to report the output of sessionInfo() and
>> > traceback(), and 3) to post a complete code example.
>>
>> > You received this message because you are subscribed to the Google Groups
>> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
