Use ImageArray package for images (and labels) #32
Artur-manr-universe.yaml
on: pull_request
R-universe testing
/
Build source pkg and vignettes
5m 32s
R-universe testing
/
Build rOpenSci docs site
R-universe testing
/
Bioconductor Checks
4m 0s
Matrix: R-universe testing / linux
Matrix: R-universe testing / macos
Matrix: R-universe testing / wasm
Matrix: R-universe testing / windows
Annotations
8 errors and 3 notices
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R-universe testing / Build source pkg and vignettes:
spatialdataR#L0
Installation OK but failed to build vignettes
* creating vignettes ... ERROR
Setting r-universe rmarkdown theme...
--- re-building ‘SpatialData.Rmd’ using rmarkdown
Loading required package: BiocStyle
Quitting from SpatialData.Rmd:169-184 [data]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `vapply()`:
! values must be length 3,
but FUN(X[[1]]) result is length 0
---
Backtrace:
▆
1. └─base::vapply(l, dim, integer(3))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SpatialData.Rmd' failed with diagnostics:
values must be length 3,
but FUN(X[[1]]) result is length 0
--- failed re-building ‘SpatialData.Rmd’
SUMMARY: processing the following file failed:
‘SpatialData.Rmd’
Error: Vignette re-building failed.
In addition: Warning message:
In tools::buildVignettes(dir = ".", tangle = TRUE) :
Files named as vignettes but with no recognized vignette engine:
‘vignettes/temp.Rmd’
(Is a VignetteBuilder field missing?)
Execution halted
If this is expected, consider precomputing your vignettes: https://ropensci.org/blog/2019/12/08/precompute-vignettes/
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R-universe testing / Build R-oldrel for MacOS:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in ‘spatialdataR-Ex.R’ failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [32s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
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R-universe testing / Build R-release for MacOS:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in ‘spatialdataR-Ex.R’ failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [45s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
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R-universe testing / Build R-release for Windows:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in 'spatialdataR-Ex.R' failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
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R-universe testing / Build R-oldrel for Windows:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in 'spatialdataR-Ex.R' failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [66s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
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R-universe testing / Build R-devel for Linux:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in ‘spatialdataR-Ex.R’ failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [55s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 8 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-devel for Windows:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in 'spatialdataR-Ex.R' failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [62s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 8 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-release for Linux:
spatialdataR#L0
Check: examples, Result: ERROR
Running examples in ‘spatialdataR-Ex.R’ failed
The error most likely occurred in:
> ### Name: extent
> ### Title: Spatial element extent
> ### Aliases: extent extent,SpatialData-method
> ### extent,SpatialDataArray-method extent,SpatialDataFrame-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="spatialdataR")
> x <- readSpatialData(x, tables=FALSE)
>
> # object-wide
> extent(x)
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [60s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
13. └─spatialdataR (local) .local(x, ...)
14. └─ImageArray::extent(data(x, NULL)) %||% ...
── Error ('test-utils.R:119:5'): extent w/ transform ───────────────────────────
Error: 'extent' is not an exported object from 'namespace:ImageArray'
Backtrace:
▆
1. ├─spatialdataR::extent(y) at test-utils.R:119:5
2. └─spatialdataR::extent(y)
3. └─spatialdataR (local) .local(x, ...)
4. └─ImageArray::extent(data(x, NULL)) %||% ...
[ FAIL 9 | WARN 0 | SKIP 0 | PASS 847 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-release for Windows
NOTICE: windows-2025 requests are being redirected to windows-2025-vs2026 by June 15, 2026
|
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R-universe testing / Build R-oldrel for Windows
NOTICE: windows-2025 requests are being redirected to windows-2025-vs2026 by June 15, 2026
|
|
R-universe testing / Build R-devel for Windows
NOTICE: windows-2025 requests are being redirected to windows-2025-vs2026 by June 15, 2026
|
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