* using log directory ‘/Users/ripley/R/packages/tests-devel/CSCDRNA.Rcheck’
* using R Under development (unstable) (2023-11-17 r85550)
* using platform: aarch64-apple-darwin23.1.0
* R was compiled by
    Apple clang version 15.0.0 (clang-1500.1.0.2.4)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Sonoma 14.1.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘CSCDRNA/DESCRIPTION’ ... OK
* this is package ‘CSCDRNA’ version ‘1.0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CSCDRNA’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... 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
* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/CSCDRNA.Rcheck/00check.log’
for details.

      123.03 real       112.95 user         7.48 sys