[BioC] unable to readImage using EBImage package

[Dan Tenenbaum]

On Sat, Mar 10, 2012 at 10:21 AM, Nurdiyanah Jambari <yanadj28 at gmail.com> wrote:
> Hi, could you explain what is EBImage vignette?
>
>
http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/doc/EBImage-installation.pdf

Also
http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/doc/EBImage-introduction.pdf
http://bioconductor.org/packages/release/bioc/manuals/EBImage/man/EBImage.pdf
All these links come from:
http://bioconductor.org/packages/release/bioc/html/EBImage.html

You can also do this within R:
browseVignettes(package="EBImage")

Dan


>
> On Sat, Mar 10, 2012 at 1:28 AM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> On Fri, Mar 9, 2012 at 4:22 AM, Nurdiyanah Jambari <yanadj28 at gmail.com>
>> wrote:
>> > Hai,
>> > I still not able to overcome my problem. I have already download the gtk
>> > from the link that you give.
>> > I'm still having the same warning/error. Can you help me?
>> >
>> >
>>
>> Did you remove the previous GTK+ installation from your system and your
>> PATH?
>> Did you add the new GTK+ installation to your PATH as documented in
>> the EBImage vignette?
>> Dan
>>
>>
>> >
>> > On Wed, Mar 7, 2012 at 2:33 PM, Nurdiyanah Jambari <yanadj28 at gmail.com>
>> > wrote:
>> >>
>> >> 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.
>> >>
>> >> 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
>> >>> >> >> >> >>
>>
>