[BioC] unable to readImage using EBImage package

[Dan Tenenbaum]

On Tue, Mar 13, 2012 at 7:42 AM, Nurdiyanah Jambari <yanadj28 at gmail.com> wrote:
> Hi,
>
> I have done all the steps suggested but still not able to fix this problem.
> Is it true that if I'm not able to open "lena.gif" that meaning the package
> is not install correctly and I wont able to open any other image from my own
> files?
>

It's probably the case that if you can't run functions on sample
images, you won't be able to run them on your own images.


> ** (<unknown>:1204): 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>:1204): GLib-GObject-CRITICAL **: file gobject.c: line 1561
> (g_object_
>
> ref): assertion `G_IS_OBJECT (object)' failed
>
> ** (<unknown>:1204): CRITICAL **: file pango-engine.c: line 68
> (_pango_engine_sh
>
> ape_shape): assertion `PANGO_IS_FONT (font)' failed
>
>

What command caused this error? Sending error messages without the
commands that caused them is not too useful.

> Can you help me explain what is the correct command to call an image, for
> example I have an image name "user186g1.tif",
> it is located in "D:\FYP\image".

What is the command you are trying to run?

For readImage(), instead of doing this:

> f = system.file("images", "lena.gif", package="EBImage")
> lena = readImage(f)

Do this:
readImage("d:/FYP/image/user186g1.tif")

system.file() is used to refer to files that are part of installed
packages. When you want to refer to your own files, you can usually
just put in the full path to your file instead of the system.file()
function.

Dan


>
> Below is the current output of my sessionInfo(EBImage):
>
>
> 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:
> character(0)
>
>
> other attached packages:
> [1] EBImage_3.10.0
>
> loaded via a namespace (and not attached):
> [1] base_2.14.1      graphics_2.14.1  grDevices_2.14.1 methods_2.14.1
> stats_2.14.1     utils_2.14.1
>
> thank you.
>
>
>
>
> --
> Nurdiyanah Bt Hj Jambari
> Student
> Faculty of Engineering
> Bachelor Engineering of Computer & Communication System Engineering
> University Putra Malaysia