[BioC] unable to readImage using EBImage package

Wolfgang Huber whuber at embl.de
Wed Mar 7 15:50:45 CET 2012 




Nurdiyanah Jambari scripsit 03/07/2012 07:33 AM:
> Can you please help me explain on how to place/install this GTK file.
> I hope I didn't wrongly place it. I've been searching in the internet, but
> there is no specific step for it.

You do not need to search the internet, reading the documentation that 
comes with the EBImage package would be a relevant first step. Have you 
followed the steps described in the vignette "EBImage installation", 
Section "Windows"?

	Best wishes
	Wolfgang


>
> thank you.
>
>
> On Wed, Mar 7, 2012 at 12:11 PM, Dan Tenenbaum<dtenenba at fhcrc.org>  wrote:
>
>> On Tue, Mar 6, 2012 at 7:25 PM, Nurdiyanah Jambari<yanadj28 at gmail.com>
>> wrote:
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Nurdiyanah Jambari<yanadj28 at gmail.com>
>>> Date: Wed, Mar 7, 2012 at 10:50 AM
>>> Subject: Re: [BioC] unable to readImage using EBImage package
>>> To: Henrik Bengtsson<hb at biostat.ucsf.edu>
>>>
>>>
>>>> library("EBImage")
>>>
>>>> sessionInfo()
>>> R version 2.14.1 (2011-12-22)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>> States.1252    LC_MONETARY=English_United States.1252
>>> LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] EBImage_3.10.0 abind_1.4-0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] tools_2.14.1
>>>
>>>
>>>
>>>
>>
>> I have found that for Windows, EBImage does not like the most recent
>> version of GTK+.
>> You should install the version specified in the EBImage installation
>> vignette:
>>
>>
>> http://ftp.gnome.org/pub/gnome/binaries/win32/gtk+/2.16/gtk+-bundle_2.16.6-20100912_win32.zip
>>
>> Dan
>>
>>
>>>
>>>
>>> On Wed, Mar 7, 2012 at 10:47 AM, Henrik Bengtsson<hb at biostat.ucsf.edu>
>>> wrote:
>>>>
>>>> They're also interested in details about EBImage, so:
>>>>
>>>>> library("EBImage");
>>>>> sessionInfo();
>>>>
>>>> Over and out.
>>>>
>>>> /Henrik
>>>>
>>>> On Tue, Mar 6, 2012 at 6:16 PM, Nurdiyanah Jambari<yanadj28 at gmail.com>
>>>> wrote:
>>>>> Sorry, I miss understood your request. This is the output of my
>>>>> sessionInfo():
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.14.1 (2011-12-22)
>>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>>
>>>>> locale:
>>>>> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
>>>>> States.1252    LC_MONETARY=English_United States.1252
>>>>> LC_NUMERIC=C
>>>>> [5] LC_TIME=English_United States.1252
>>>>>
>>>>> attached base packages:
>>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Mar 7, 2012 at 9:42 AM, Dan Tenenbaum<dtenenba at fhcrc.org>
>>>>> wrote:
>>>>>
>>>>>> On Tue, Mar 6, 2012 at 4:35 PM, Nurdiyanah Jambari<
>> yanadj28 at gmail.com>
>>>>>> wrote:
>>>>>>> Sorry, I forgot to mention that the system will go to not
>> responding
>>>>>>> and
>>>>>>> need to be closed after the pop-up message appear.
>>>>>>>
>>>>>>
>>>>>> Please post the output of sessionInfo(), run it immediately before
>> the
>>>>>> command that causes the error.
>>>>>>
>>>>>> Thanks,
>>>>>> Dan
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Mar 7, 2012 at 8:30 AM, Dan Tenenbaum<dtenenba at fhcrc.org>
>>>>>> wrote:
>>>>>>>>
>>>>>>>> On Tue, Mar 6, 2012 at 4:26 PM, Nurdiyanah Jambari
>>>>>>>> <yanadj28 at gmail.com>
>>>>>>>> wrote:
>>>>>>>>> This error happen while I'm trying to view the example image.
>>>>>>>>> These is
>>>>>>>>> because I read from the manual, if I want to make sure that the
>>>>>> package
>>>>>>>>> is
>>>>>>>>> install correctly, it should be able to display the "lena.gif"
>>>>>>>>> image:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> library("EBImage")
>>>>>>>>>> f = system.file("images", "lena.gif", package="EBImage")
>>>>>>>>>> lena = readImage(f)
>>>>>>>>>> display(lena)
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Please post the output of
>>>>>>>> sessionInfo()
>>>>>>>> Thanks
>>>>>>>> Dan
>>>>>>>>
>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Wed, Mar 7, 2012 at 3:14 AM, Dan Tenenbaum<
>> dtenenba at fhcrc.org>
>>>>>>>>> wrote:
>>>>>>>>>>
>>>>>>>>>> On Tue, Mar 6, 2012 at 12:39 AM, Nurdiyanah Jambari
>>>>>>>>>> <yanadj28 at gmail.com>
>>>>>>>>>> wrote:
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> Please help me with these problem. Every time I'm trying to
>>>>>>>>>>> display
>>>>>>>>>>> the
>>>>>>>>>>> example image, I receive these kind of pop-up warning:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> ** (<unknown>:2932): WARNING **: No builtin or dynamically
>>>>>>>>>>> loaded
>>>>>>>>>>> modules
>>>>>>>>>>> were found. Pango will not work correctly. This probably
>> means
>>>>>>>>>>> there was an error in the creation of:
>>>>>>>>>>>    'C:\Windows\system32\etc\pango\pango.modules'
>>>>>>>>>>> You may be able to recreate this file by running
>>>>>> pango-querymodules.
>>>>>>>>>>>
>>>>>>>>>>> (<unknown>:2932): GLib-GObject-CRITICAL **: file gobject.c:
>>>>>>>>>>> line
>>>>>> 1561
>>>>>>>>>>> (g_object_
>>>>>>>>>>> ref): assertion `G_IS_OBJECT (object)' failed
>>>>>>>>>>>
>>>>>>>>>>> ** (<unknown>:2932): CRITICAL **: file pango-engine.c: line
>> 68
>>>>>>>>>>> (_pango_engine_sh
>>>>>>>>>>> ape_shape): assertion `PANGO_IS_FONT (font)' failed
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> I have try several method that I found searching from the
>>>>>>>>>>> internet,
>>>>>>>>>>> but
>>>>>>>>>>> still I could not fix these problem.
>>>>>>>>>>
>>>>>>>>>> It's difficult for us to help without knowing the exact
>> commands
>>>>>>>>>> you
>>>>>>>>>> tried that caused this error, and more information about your
>>>>>>>>>> system
>>>>>>>>>> (e.g., the output of the sessionInfo() function).
>>>>>>>>>>
>>>>>>>>>> Dan
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Nurdiyanah Bt Hj Jambari
>>>>>>>>>>> Student
>>>>>>>>>>> Faculty of Engineering
>>>>>>>>>>> Bachelor Engineering of Computer&  Communication System
>>>>>>>>>>> Engineering
>>>>>>>>>>> University Putra Malaysia
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Nurdiyanah Bt Hj Jambari
>>>>>>>>> Student
>>>>>>>>> Faculty of Engineering
>>>>>>>>> Bachelor Engineering of Computer&  Communication System
>>>>>>>>> Engineering
>>>>>>>>> University Putra Malaysia
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Nurdiyanah Bt Hj Jambari
>>>>>>> Student
>>>>>>> Faculty of Engineering
>>>>>>> Bachelor Engineering of Computer&  Communication System Engineering
>>>>>>> University Putra Malaysia
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Nurdiyanah Bt Hj Jambari
>>>>> Student
>>>>> Faculty of Engineering
>>>>> Bachelor Engineering of Computer&  Communication System Engineering
>>>>> University Putra Malaysia
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
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>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>>
>>>
>>> --
>>> Nurdiyanah Bt Hj Jambari
>>> Student
>>> Faculty of Engineering
>>> Bachelor Engineering of Computer&  Communication System Engineering
>>> University Putra Malaysia
>>>
>>>
>>>
>>> --
>>> Nurdiyanah Bt Hj Jambari
>>> Student
>>> Faculty of Engineering
>>> Bachelor Engineering of Computer&  Communication System Engineering
>>> University Putra Malaysia
>>
>
>
>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber

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