S3 reading support #11
Bisaloor-universe.yaml
on: pull_request
R-universe testing
/
Build source pkg and vignettes
5m 45s
R-universe testing
/
Build rOpenSci docs site
0s
R-universe testing
/
Bioconductor Checks
3m 31s
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:
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:263-283 [crop]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! unable to find an inherited method for function 'instance_key' for signature 'x = "NULL"'
---
Backtrace:
▆
1. ├─SpatialData::crop(sd, xy)
2. └─SpatialData::crop(sd, xy)
3. └─SpatialData (local) .local(x, y, ...)
4. └─base::lapply(...)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. ├─base::data.frame(r = regions(t), i = instances(t), keep = seq_len(ncol(t)))
7. ├─SpatialData::instances(t)
8. └─SpatialData::instances(t)
9. └─SpatialData (local) .local(x, ...)
10. ├─SpatialData::instance_key(x)
11. └─SpatialData::instance_key(x)
12. └─SpatialData (local) .local(x, ...)
13. └─SpatialData::instance_key(meta(x))
14. └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'SpatialData.Rmd' failed with diagnostics:
unable to find an inherited method for function 'instance_key' for signature 'x = "NULL"'
--- 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-oldrel for MacOS:
SpatialData#L0
Check: examples, Result: ERROR
Running examples in ‘SpatialData-Ex.R’ failed
The error most likely occurred in:
> ### Name: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
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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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
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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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
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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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
|
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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: CTgraph
> ### Title: Coord. trans. graph
> ### Aliases: CTgraph CTpath CTplot CTgraph,SpatialData-method
> ### CTgraph,SpatialDataElement-method CTgraph,ANY-method
> ### CTpath,SpatialData-method CTpath,SpatialDataElement-method
> ### CTpath,ANY-method
>
> ### ** Examples
>
> x <- file.path("extdata", "blobs.zarr")
> x <- system.file(x, package="SpatialData")
> x <- readSpatialData(x, tables=FALSE)
Error in Rarr:::.read_array_metadata(zarr_path, metadata_file, s3_client = s3_client) :
unused argument (metadata_file)
Calls: readSpatialData ... lapply -> FUN -> ZarrArraySeed -> get_zarr_metadata
Execution halted
Check: tests, Result: ERROR
Running ‘testthat.R’ [9s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
1. └─SpatialData::readSpatialData(zs) at test-validity.R:6:1
2. └─base::lapply(ls, .readLayer)
3. └─SpatialData (local) FUN(X[[i]], ...)
4. └─base::lapply(j, reader)
5. └─SpatialData (local) FUN(X[[i]], ...)
6. └─SpatialData:::.readArray(x, ...)
7. └─base::lapply(ds, ZarrArray)
8. └─ZarrArray (local) FUN(X[[i]], ...)
9. └─ZarrArray::ZarrArraySeed(zarr_path, s3_client = s3_client)
10. └─ZarrArray:::get_zarr_metadata(zarr_path, s3_client = s3_client)
[ FAIL 16 | WARN 0 | SKIP 0 | PASS 0 ]
Error:
! Test failures.
Execution halted
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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
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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
|
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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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