Last updated on 2023-11-20 09:49:20 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.3 | ERROR | ||||
| r-devel-linux-x86_64-debian-gcc | 1.0.3 | 45.96 | 345.09 | 391.05 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.3 | 683.93 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.3 | 633.43 | ERROR | |||
| r-devel-windows-x86_64 | 1.0.3 | 46.00 | 307.00 | 353.00 | ERROR | |
| r-patched-linux-x86_64 | 1.0.3 | 38.18 | 447.78 | 485.96 | ERROR | |
| r-release-linux-x86_64 | 1.0.3 | 47.56 | 444.96 | 492.52 | ERROR | |
| r-release-macos-arm64 | 1.0.3 | 157.00 | OK | |||
| r-release-macos-x86_64 | 1.0.3 | 282.00 | OK | |||
| r-release-windows-x86_64 | 1.0.3 | 60.00 | 402.00 | 462.00 | ERROR | |
| r-oldrel-macos-arm64 | 1.0.3 | 141.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.3 | 191.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.3 | 58.00 | 361.00 | 419.00 | ERROR |
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘CSCDRNA-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: example_data
> ### Title: Example data
> ### Aliases: example_data
> ### Keywords: datasets
>
> ### ** Examples
>
> # Load example data.
> data(example_data)
>
> # Build ExpressionSet with bulk data.
> bulk.eset <- Biobase::ExpressionSet(assayData = example_data$bulk.matrix)
>
> # Build ExpressionSet with single-cell data.
> sc.counts.matrix=example_data$sc.counts.matrix
> individual.labels=example_data$individual.labels
> cell.type.labels=example_data$cell.type.labels
> sample.ids <- colnames(sc.counts.matrix)
> # individual.labels and cell.types should be in the same order as in sample.ids.
> sc.pheno <- data.frame(check.names=FALSE, check.rows=FALSE,
+ stringsAsFactors=FALSE,row.names=sample.ids,
+ SubjectName=individual.labels,cellType=cell.type.labels)
> sc.meta <- data.frame(labelDescription=c("SubjectName","cellType"),
+ row.names=c("SubjectName","cellType"))
> sc.pdata <- new("AnnotatedDataFrame",data=sc.pheno, varMetadata=sc.meta)
> sc.eset <- Biobase::ExpressionSet(assayData=sc.counts.matrix,phenoData=sc.pdata)
>
> # Run CSCD on the example data.
> analysis <- CSCD(bulk.eset=bulk.eset,sc.eset= sc.eset,
+ min.p=0.3,markers=NULL,cell.types="cellType",
+ subj.names="SubjectName",verbose=TRUE)
Decomposing into 4 cell types.
Warning: Data is of class matrix. Coercing to dgCMatrix.
Calculating cluster CT1
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT2
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT3
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT4
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Warning: No DE genes identified
Warning: The following tests were not performed:
Warning: When testing CT1 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT2 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT3 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT4 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: CSCD -> FindAllMarkers_filter.by.cluster -> colnames<-
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 1.0.3
Check: examples
Result: ERROR
Running examples in ‘CSCDRNA-Ex.R’ failed
The error most likely occurred in:
> ### Name: example_data
> ### Title: Example data
> ### Aliases: example_data
> ### Keywords: datasets
>
> ### ** Examples
>
> # Load example data.
> data(example_data)
>
> # Build ExpressionSet with bulk data.
> bulk.eset <- Biobase::ExpressionSet(assayData = example_data$bulk.matrix)
>
> # Build ExpressionSet with single-cell data.
> sc.counts.matrix=example_data$sc.counts.matrix
> individual.labels=example_data$individual.labels
> cell.type.labels=example_data$cell.type.labels
> sample.ids <- colnames(sc.counts.matrix)
> # individual.labels and cell.types should be in the same order as in sample.ids.
> sc.pheno <- data.frame(check.names=FALSE, check.rows=FALSE,
+ stringsAsFactors=FALSE,row.names=sample.ids,
+ SubjectName=individual.labels,cellType=cell.type.labels)
> sc.meta <- data.frame(labelDescription=c("SubjectName","cellType"),
+ row.names=c("SubjectName","cellType"))
> sc.pdata <- new("AnnotatedDataFrame",data=sc.pheno, varMetadata=sc.meta)
> sc.eset <- Biobase::ExpressionSet(assayData=sc.counts.matrix,phenoData=sc.pdata)
>
> # Run CSCD on the example data.
> analysis <- CSCD(bulk.eset=bulk.eset,sc.eset= sc.eset,
+ min.p=0.3,markers=NULL,cell.types="cellType",
+ subj.names="SubjectName",verbose=TRUE)
Decomposing into 4 cell types.
Warning: Data is of class matrix. Coercing to dgCMatrix.
Calculating cluster CT1
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT2
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT3
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Calculating cluster CT4
Warning: No layers found matching search pattern provided
Warning: Layer ‘data’ is empty
Warning: Layer ‘data’ is empty
Warning: No DE genes identified
Warning: The following tests were not performed:
Warning: When testing CT1 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT2 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT3 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Warning: When testing CT4 versus all:
error in evaluating the argument 'x' in selecting a method for function 'rowSums': subscript out of bounds
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [0]
Calls: CSCD -> FindAllMarkers_filter.by.cluster -> colnames<-
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64