[BioC] EBImage Sample code errors

[Dan Tenenbaum]

On Wed, Jul 18, 2012 at 4:39 PM, Robert Baer <rbaer at 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 at 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

What happens if you open a command window and type

echo %PATH%

also, what about this command:

convert

?
Dan


>> R.Version()
> $platform
> [1] "i386-pc-mingw32"
>
> $arch
> [1] "i386"
>
> $os
> [1] "mingw32"
>
> $system
> [1] "i386, mingw32"
>
> $status
> [1] ""
>
> $major
> [1] "2"
>
> $minor
> [1] "15.1"
>
> $year
> [1] "2012"
>
> $month
> [1] "06"
>
> $day
> [1] "22"
>
> $`svn rev`
> [1] "59607"
>
> $language
> [1] "R"
>
> $version.string
> [1] "R version 2.15.1 (2012-06-22)"
>
> $nickname
> [1] "Roasted Marshmallows"
>
>
>>
>
>>> Did something go from S3 to S4 that changes the way this code should be
>>> written?
>>>
>>> Thanks,
>>>
>>> Rob
>>>
>>>
>>>
>>>          [[alternative HTML version deleted]]
>>>
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>
>
>