Use r-universe workflow for R CMD check and BiocCheck #1
Bisaloor-universe.yaml
on: pull_request
R-universe testing
/
Build source pkg and vignettes
5m 37s
R-universe testing
/
Build rOpenSci docs site
R-universe testing
/
Bioconductor Checks
0s
Matrix: R-universe testing / linux
Matrix: R-universe testing / macos
Matrix: R-universe testing / wasm
Matrix: R-universe testing / windows
Annotations
9 errors and 3 notices
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R-universe testing / Build source pkg and vignettes:
SpatialData#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:79-90 [load]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `base::table()`:
! all arguments must have the same length
---
Backtrace:
▆
1. └─SpatialData::readSpatialData(zs)
2. ├─base::do.call(SpatialData, sd)
3. └─SpatialData (local) `<fn>`(...)
4. └─SpatialData::.SpatialData(...)
5. └─methods::new(`<chr>`, ...)
6. ├─methods::initialize(value, ...)
7. └─methods::initialize(value, ...)
8. └─methods::validObject(.Object)
9. ├─methods (local) anyStrings(validityMethod(object))
10. │ └─base::isTRUE(x)
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SpatialData.Rmd' failed with diagnostics:
all arguments must have the same length
--- failed re-building ‘SpatialData.Rmd’
SUMMARY: processing the following file failed:
‘SpatialData.Rmd’
Error: Vignette re-building failed.
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-release for MacOS:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in ‘SpatialData-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [19s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
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R-universe testing / Build R-oldrel for MacOS:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in ‘SpatialData-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [17s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
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R-universe testing / Build R-release for Windows:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in 'SpatialData-Ex.R' failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-oldrel for Windows:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in 'SpatialData-Ex.R' failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-release for Linux:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in ‘SpatialData-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [18s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
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R-universe testing / Build R-devel for Windows:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in 'SpatialData-Ex.R' failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
|
|
R-universe testing / Build R-devel for Linux:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in ‘SpatialData-Ex.R’ failed
The error most likely occurred in:
> ### Name: SpatialData-class
> ### Title: The 'SpatialData' class
> ### Aliases: SpatialData-class .SpatialData SpatialData data meta layer
> ### element element<- image label point shape table,ANY-method images
> ### labels points shapes tables image<- label<- point<- shape<- table<-
> ### images<- labels<- points<- shapes<- tables<- imageNames labelNames
> ### pointNames shapeNames tableNames imageNames<- labelNames<-
> ### pointNames<- shapeNames<- tableNames<-
> ### [[<-,SpatialData,character,ANY-method
> ### [[<-,SpatialData,numeric,ANY-method $,SpatialData-method
> ### $<-,SpatialData-method [[,SpatialData,numeric,ANY-method
> ### [[,SpatialData,character,ANY-method data,ANY-method
> ### meta,SpatialDataElement-method [,SpatialData,ANY,ANY,ANY-method
> ### rownames,SpatialData-method colnames,SpatialData-method
> ### layer,SpatialData,character-method layer,SpatialData,ANY-method
> ### element,SpatialData,character-method
> ### element,SpatialData,numeric-method element,SpatialData,missing-method
> ### element,SpatialData,ANY-method element<-,SpatialData,character-method
> ### images,SpatialData-method labels,SpatialData-method
> ### points,SpatialData-method shapes,SpatialData-method
> ### tables,SpatialData-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> (x <- readSpatialData(x))
Error in base::table(object, i) : all arguments must have the same length
Calls: readSpatialData ... table -> table -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [23s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
11. └─S4Vectors (local) validityMethod(object)
12. └─SpatialData (local) method(object)
13. └─SpatialData:::.validateTables(x)
14. ├─SpatialData (local) sce(se <- table(object, i))
15. │ └─methods::is(., "SingleCellExperiment")
16. ├─BiocGenerics::table(object, i)
17. ├─BiocGenerics::table(object, i)
18. │ └─base::eval(sys_call, envir = parent.frame())
19. │ └─base::eval(sys_call, envir = parent.frame())
20. └─base::table(object, i)
[ FAIL 11 | WARN 0 | SKIP 0 | PASS 234 ]
Error:
! Test failures.
Execution halted
|
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R-universe testing / Build R-release for Wasm
Process completed with exit code 1.
|
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R-universe testing / Build R-release for Windows
NOTICE: windows-2025 requests are being redirected to windows-2025-vs2026 by June 15, 2026
|
|
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
|