Last updated on 2025-12-14 04:50:22 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| CMGFM | 13 | ||
| COAP | 13 | ||
| coFAST | 6 | 7 | |
| DR.SC | 4 | 2 | 7 |
| GFM | 13 | ||
| MMGFM | 2 | 11 | |
| MultiCOAP | 13 | ||
| MultiRFM | 13 | ||
| PRECAST | 4 | 2 | 7 |
| ProFAST | 4 | 2 | 7 |
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 6, OK: 7
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘coFAST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NCFM
> ### Title: Cell-feature coembedding for scRNA-seq data
> ### Aliases: NCFM
>
> ### ** Examples
>
> data(pbmc3k_subset)
> pbmc3k_subset <- NCFM(pbmc3k_subset)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─coFAST::NCFM(pbmc3k_subset)
2. ├─base::as.matrix(...)
3. ├─Seurat::GetAssayData(object = object, slot = slot, assay = assay)
4. └─SeuratObject:::GetAssayData.Seurat(...)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘coFAST-Ex.R’ failed
The error most likely occurred in:
> ### Name: NCFM
> ### Title: Cell-feature coembedding for scRNA-seq data
> ### Aliases: NCFM
>
> ### ** Examples
>
> data(pbmc3k_subset)
> pbmc3k_subset <- NCFM(pbmc3k_subset)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─coFAST::NCFM(pbmc3k_subset)
2. ├─base::as.matrix(...)
3. ├─Seurat::GetAssayData(object = object, slot = slot, assay = assay)
4. └─SeuratObject:::GetAssayData.Seurat(...)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64
Version: 0.1.0
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: ‘scater’
Flavor: r-oldrel-macos-arm64
Version: 0.1.0
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavor: r-oldrel-macos-arm64
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 3.6
Check: examples
Result: ERROR
Running examples in ‘DR.SC-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DR.SC
> ### Title: Joint dimension reduction and spatial clustering
> ### Aliases: DR.SC DR.SC.Seurat
> ### Keywords: Dimension reduction Spatial clustering
>
> ### ** Examples
>
>
> ## we generate the spatial transcriptomics data with lattice neighborhood, i.e. ST platform.
> data(seu)
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp
Attaching package: ‘SeuratObject’
The following objects are masked from ‘package:base’:
intersect, t
> seu <- NormalizeData(seu, verbose=FALSE)
> # choose 100 highly variable features
> # seu <- FindVariableFeatures(seu, nfeatures = 100)
> # maxIter = 2 is only used for illustration, and user can use default.
> # seu1 <- DR.SC(seu, K=4, platform = 'ST', maxIter=2,verbose=FALSE)
>
> # choose spatially variable features (SVGs)
> seu <- FindSVGs(seu, nfeatures = 40, verbose=FALSE)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─DR.SC::FindSVGs(seu, nfeatures = 40, verbose = FALSE)
2. ├─SeuratObject::GetAssayData(seu, assay = assay, slot = "counts")
3. └─SeuratObject:::GetAssayData.Seurat(seu, assay = assay, slot = "counts")
4. └─SeuratObject::.Deprecate(...)
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 3.6
Check: examples
Result: ERROR
Running examples in ‘DR.SC-Ex.R’ failed
The error most likely occurred in:
> ### Name: DR.SC
> ### Title: Joint dimension reduction and spatial clustering
> ### Aliases: DR.SC DR.SC.Seurat
> ### Keywords: Dimension reduction Spatial clustering
>
> ### ** Examples
>
>
> ## we generate the spatial transcriptomics data with lattice neighborhood, i.e. ST platform.
> data(seu)
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp
Attaching package: ‘SeuratObject’
The following objects are masked from ‘package:base’:
intersect, t
> seu <- NormalizeData(seu, verbose=FALSE)
> # choose 100 highly variable features
> # seu <- FindVariableFeatures(seu, nfeatures = 100)
> # maxIter = 2 is only used for illustration, and user can use default.
> # seu1 <- DR.SC(seu, K=4, platform = 'ST', maxIter=2,verbose=FALSE)
>
> # choose spatially variable features (SVGs)
> seu <- FindSVGs(seu, nfeatures = 40, verbose=FALSE)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─DR.SC::FindSVGs(seu, nfeatures = 40, verbose = FALSE)
2. ├─SeuratObject::GetAssayData(seu, assay = assay, slot = "counts")
3. └─SeuratObject:::GetAssayData.Seurat(seu, assay = assay, slot = "counts")
4. └─SeuratObject::.Deprecate(...)
5. └─lifecycle::deprecate_stop(...)
6. └─lifecycle:::deprecate_stop0(msg)
7. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 3.6
Check: installed package size
Result: NOTE
installed size is 11.5Mb
sub-directories of 1Mb or more:
data 3.2Mb
libs 8.0Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: NOTE: 2, OK: 11
Version: 1.2.1
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘GFM’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Current CRAN status: OK: 13
Current CRAN status: OK: 13
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 1.7
Check: examples
Result: ERROR
Running examples in ‘PRECAST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CreatePRECASTObject
> ### Title: Create the PRECAST object with preprocessing step.
> ### Aliases: CreatePRECASTObject
>
> ### ** Examples
>
> data(PRECASTObj)
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp
Attaching package: ‘SeuratObject’
The following objects are masked from ‘package:base’:
intersect, t
> seuList <- PRECASTObj@seulist
> ## Check the input of seuList for create PRECAST object.
> ## Check the default assay for each data batch
> lapply(seuList, DefaultAssay)
[[1]]
[1] "RNA"
[[2]]
[1] "RNA"
> ## Check the spatial coordinates in the meta data named "row" and "col".
> head(seuList[[1]]@meta.data)
orig.ident nCount_RNA nFeature_RNA row col true_cluster
cell1_1 cell1 10004 55 1 1 2
cell1_2 cell1 12614 54 2 1 2
cell1_3 cell1 18233 57 3 1 2
cell1_4 cell1 1726 50 4 1 7
cell1_5 cell1 3451 53 5 1 7
cell1_6 cell1 134457 60 6 1 6
> ## Then create PRECAST object using this seuList.
> ## For convenience, we show the user-specified genes' list for creating PRECAST object.
> ## Users can use SVGs from SPARK-X or HVGs.
> PRECASTObj2 <- CreatePRECASTObject(seuList,
+ customGenelist= row.names(seuList[[1]]), verbose=FALSE)
Error in FUN(X[[i]], ...) :
filter_gene: Seuat object must provide slots count or data in assay!
Calls: CreatePRECASTObject -> <Anonymous> -> lapply -> FUN
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.7
Check: examples
Result: ERROR
Running examples in ‘PRECAST-Ex.R’ failed
The error most likely occurred in:
> ### Name: CreatePRECASTObject
> ### Title: Create the PRECAST object with preprocessing step.
> ### Aliases: CreatePRECASTObject
>
> ### ** Examples
>
> data(PRECASTObj)
> library(Seurat)
Loading required package: SeuratObject
Loading required package: sp
Attaching package: ‘SeuratObject’
The following objects are masked from ‘package:base’:
intersect, t
> seuList <- PRECASTObj@seulist
> ## Check the input of seuList for create PRECAST object.
> ## Check the default assay for each data batch
> lapply(seuList, DefaultAssay)
[[1]]
[1] "RNA"
[[2]]
[1] "RNA"
> ## Check the spatial coordinates in the meta data named "row" and "col".
> head(seuList[[1]]@meta.data)
orig.ident nCount_RNA nFeature_RNA row col true_cluster
cell1_1 cell1 10004 55 1 1 2
cell1_2 cell1 12614 54 2 1 2
cell1_3 cell1 18233 57 3 1 2
cell1_4 cell1 1726 50 4 1 7
cell1_5 cell1 3451 53 5 1 7
cell1_6 cell1 134457 60 6 1 6
> ## Then create PRECAST object using this seuList.
> ## For convenience, we show the user-specified genes' list for creating PRECAST object.
> ## Users can use SVGs from SPARK-X or HVGs.
> PRECASTObj2 <- CreatePRECASTObject(seuList,
+ customGenelist= row.names(seuList[[1]]), verbose=FALSE)
Error in FUN(X[[i]], ...) :
filter_gene: Seuat object must provide slots count or data in assay!
Calls: CreatePRECASTObject -> <Anonymous> -> lapply -> FUN
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.7
Check: installed package size
Result: NOTE
installed size is 11.8Mb
sub-directories of 1Mb or more:
data 2.2Mb
libs 8.8Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 4, NOTE: 2, OK: 7
Version: 1.6
Check: examples
Result: ERROR
Running examples in ‘ProFAST-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NCFM
> ### Title: Cell-feature coembedding for scRNA-seq data
> ### Aliases: NCFM
>
> ### ** Examples
>
> data(pbmc3k_subset)
> pbmc3k_subset <- NCFM(pbmc3k_subset)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─ProFAST::NCFM(pbmc3k_subset)
2. ├─base::as.matrix(...)
3. ├─Seurat::GetAssayData(object = object, slot = slot, assay = assay)
4. └─SeuratObject:::GetAssayData.Seurat(...)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-release-linux-x86_64
Version: 1.6
Check: examples
Result: ERROR
Running examples in ‘ProFAST-Ex.R’ failed
The error most likely occurred in:
> ### Name: NCFM
> ### Title: Cell-feature coembedding for scRNA-seq data
> ### Aliases: NCFM
>
> ### ** Examples
>
> data(pbmc3k_subset)
> pbmc3k_subset <- NCFM(pbmc3k_subset)
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject
5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Backtrace:
▆
1. └─ProFAST::NCFM(pbmc3k_subset)
2. ├─base::as.matrix(...)
3. ├─Seurat::GetAssayData(object = object, slot = slot, assay = assay)
4. └─SeuratObject:::GetAssayData.Seurat(...)
5. └─SeuratObject::.Deprecate(...)
6. └─lifecycle::deprecate_stop(...)
7. └─lifecycle:::deprecate_stop0(msg)
8. └─rlang::cnd_signal(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 1.6
Check: installed package size
Result: NOTE
installed size is 15.8Mb
sub-directories of 1Mb or more:
data 2.2Mb
libs 13.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64