Dear Robert,

The issue you're mentioning seems to be a Windows-specific bug that we
don't see when building the Linux version of the package.
I'm having a look.
Thanks,

Greg

On Thu, Jul 19, 2012 at 8:31 AM, Robert Baer <rbaer@atsu.edu> wrote:

> On 7/18/2012 6:51 PM, Dan Tenenbaum wrote:
>
>> On Wed, Jul 18, 2012 at 4:39 PM, Robert Baer <rbaer@atsu.edu> wrote:
>>
>>> On 7/18/2012 5:59 PM, Dan Tenenbaum wrote:
>>>
>>>> On Wed, Jul 18, 2012 at 3:36 PM, Robert Baer <rbaer@atsu.edu> wrote:
>>>>
>>>>> I get the following errors when running the EBImage introductory sample
>>>>> code:
>>>>>
>>>>>  ##############################**#####################
>>>>>> ### code chunk number 11: math2
>>>>>> ##############################**#####################
>>>>>> lena4 = lena[299:376, 224:301]
>>>>>>
>>>>> Error in slot(lena, ".Data")[299:376, 224:301] :
>>>>>      incorrect number of dimensions
>>>>>
>>>>>> lena5 = lena>0.5
>>>>>> lena6 = t(lena)
>>>>>>
>>>>> Error in t.default(lena) : argument is not a matrix
>>>>>
>>>>>> print(median(lena))
>>>>>>
>>>>> [1] 0.3803922
>>>>> Can any when help me understand what is going on?
>>>>>
>>>>>  Can you send the output of sessionInfo() after receiving this error?
>>>> Dan
>>>>
>>>>  Sorry!  I should have done this in the first place :-(
>>>
>>>  sessionInfo()
>>>>
>>> R version 2.15.1 (2012-06-22)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252
>>> [2] LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252
>>> [4] 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_3.12.0 abind_1.4-0
>>>
>> Our Windows release build machine has the same sessionInfo() after
>> loading EBImage, it builds this vignette just fine. So I wonder if it
>> is a problem with the external dependencies GTK+ and ImageMagick. I
>> assume you installed them as described here:
>> http://bioconductor.org/**packages/release/bioc/**
>> vignettes/EBImage/inst/doc/**EBImage-installation.pdf<http://bioconductor.org/packages/release/bioc/vignettes/EBImage/inst/doc/EBImage-installation.pdf>
>>
>> What happens if you open a command window and type
>>
>> echo %PATH%
>>
>> also, what about this command:
>>
>> convert
>>
> Thanks for the useful ideas Dan, but I have not yet made useful progress.
> To answer your follow-up queries:
>
> C:\Users\rbaer>echo %path%
> C:\GTK\bin;C:\Program Files (x86)\ImageMagick-6.7.8-Q16;C:**
> \Windows\system32;C:\Windows;**C:\Windows\System32\Wbem;C:\**
> Windows\System32\**WindowsPowerShell\v1.0\;C:\**Program Files\ggobi;
>
> Typing 'convert' at the command prompt produces an extensive list of what
> appear to be possible flags for imageMagick
>
> I am using a 64-bit Windows 7 (Enterprise edition) OS but the 32-bit R
> when I get this error.  I think both the ImageMagick and GTK+ are designed
> for 32-bit, and should therefore match the R I'm using.
>
> Just for clarification, the whole vignette runs just as expected EXCEPT
> for code chunk 11 where lena4 and lena6 are supposedly created and code
> chunk 12 when lena4 and lena6 are supposedly saved (because they didn't
> create.  lena5 works fine.  Both fail with the errors indicated above.  The
> rest of the code runs and produces images as expected (or at least without
> error and with images appearing and/or getting saved).  lena6 is created in
> the vignette code as a transpose of lena (an "image" object) ostensibly
> because it is not a matrix.  It appears that this line of code is using
> t.default suggesting that this generic function doesn't have an "Image"
> method.  Should it?  Would this be a method supplied by EBImage or some
> other package?  This makes me suspect some sort of R issue, but I don't
> know enough about GTK+ or ImageMagick to eliminate issues there.
>
> # Version notation.    EBImage_3.12.0 abind_1.4-0
> # structure and class of the lena object that fails when I attempt to make
> lena4 & lena6 objects
> > str(lena)
> Formal class 'Image' [package "EBImage"] with 2 slots
>   ..@ .Data    : num [1:512, 1:512, 1:3] 0.537 0.537 0.537 0.533 0.541 ...
>   ..@ colormode: int 2
>
> > class(lena)
> [1] "Image"
> attr(,"package")
> [1] "EBImage"
> >
>
> # The installation instructions provide the following:
> # System Requirements    ImageMagick (>= 6.3.7), GTK+ (> 2.6)
> # I have:
> # ImageMagick 6.7.8-2 Q16(2012-07-01)
> # GTk+ Runtime Environment 2.10.11-1
> #
> # The computer is a 64-bit windows 7 OS running R i386-pc-mingw32/i386
> (32-bit)
>
>
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