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
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Hervé Pagès
Bioconductor Core Team
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