[Bioc-devel] SpatialExperiment checks fail on Windows platform

[Dario Righelli]

Hi Harvè,

thanks for your reply and suggestion, we'll definitively try what you 
suggested.

Dario

Il 13/12/22 20:57, Hervé Pagès ha scritto:
> Hi Dario,
>
> Note that we observe the same problem on our daily Windows builder, so 
> this has not much to do with your GitHub actions setup:
>
> https://bioconductor.org/checkResults/3.17/bioc-LATEST/SpatialExperiment/palomino3-buildsrc.html 
>
>
> It looks to me that some recent changes to the package broke the dim() 
> method for StoredSpatialImage objects. Here is how the method is 
> defined in BioC devel:
>
> > selectMethod("dim", "StoredSpatialImage")
> Object with tracing code, class "MethodDefinitionWithTrace"
> Original definition:
> Method Definition:
>
> function (x)
> {
>     src <- imgSource(x)
>     src <- normalizePath(src)
>     src <- paste0("file://", src)
>     img <- .get_from_cache(src, NULL)
>     if (!is.null(img))
>         return(dim(img))
>     img <- image_read(src)
>     tib <- image_info(img)
>     c(tib$height, tib$width)
> }
> <bytecode: 0x55a3f2dee5b8>
> <environment: namespace:SpatialExperiment>
>
> Signatures:
>         x
> target  "StoredSpatialImage"
> defined "StoredSpatialImage"
>
> ## (to see the tracing code, look at body(object))
>
> I'm not sure I understand the logic for prefixing the already 
> normalized local path with "file://", but this breaks 
> magick::image_read() on Windows. Without the "file://" prefix, the 
> dim() method seems to work fine on all platforms.
>
> Hope this helps,
>
> H.
>
> On 12/12/2022 02:11, Dario Righelli wrote:
>> Hi everyone,
>>
>> we are having an issue when running GithubActions on Windows platform
>> that we are not able to figure out.
>>
>> The error is about loading an image as a grob during the vignette
>> construction.
>> It seems that it loads the image path twice, but this sounds weird
>> because the same vignette code is working on the other two platforms
>> (linux and osx).
>>
>> Does anyone have any ideas about this?
>>
>> Here it is the reported check error:
>>
>> Quitting from lines 110-111 (SpatialExperiment.Rmd) Error: processing
>> vignette 'SpatialExperiment.Rmd' failed with diagnostics: Rscript.exe:
>> UnableToOpenBlob
>> `F:\biocbuild\bbs-3.17-bioc\tmpdir\RtmpsN0lzb\Rbuild3f6c3ae24a46\SpatialExperiment\vignettes\file:\F:\biocbuild\bbs-3.17-bioc\tmpdir\RtmpsN0lzb\Rinst3f6c113c6bc2\SpatialExperiment\extdata\10xVisium\section1\outs\spatial\tissue_lowres_image.png': 
>>
>> Invalid argument @ error/blob.c/OpenBlob/2924 --- failed re-building
>> 'SpatialExperiment.Rmd'
>>
>> Thanks, Dario
>>
>>     [[alternative HTML version deleted]]
>>
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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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