* using log directory 'd:/Rcompile/CRANpkg/local/3.6/VAM.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'VAM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VAM' version '0.5.2'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'VAM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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 ... [7s] 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'VAM-Ex.R' failed
The error most likely occurred in:

> ### Name: vamForSeurat
> ### Title: VAM wrapper for scRNA-seq data processed using the Seurat
> ###   framework
> ### Aliases: vamForSeurat
> ### Keywords: file
> 
> ### ** Examples
> 
>     # Only run example code if Seurat package is available
>     if (requireNamespace("Seurat", quietly=TRUE) & requireNamespace("SeuratObject", quietly=TRUE)) {
+         # Define a collection with one gene set for the first 10 genes
+         collection=list(set1=1:10)
+         # Execute on the pbmc_small scRNA-seq data set included with SeuratObject
+         # See vignettes for more detailed Seurat examples
+         vamForSeurat(seurat.data=SeuratObject::pbmc_small,
+             gene.set.collection=collection)
+     }
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  7.44 0.53 8.36 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')

runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [34s] WARNING
Error(s) in re-building vignettes:
--- re-building 'VAM_PBMC3K_Hallmark_LogNormalization.Rnw' using Sweave
--- finished re-building 'VAM_PBMC3K_Hallmark_LogNormalization.Rnw'

--- re-building 'VAM_PBMC3K_LogNormalization.Rnw' using Sweave
--- finished re-building 'VAM_PBMC3K_LogNormalization.Rnw'

--- re-building 'VAM_PBMC3K_SCTransform.Rnw' using Sweave
--- finished re-building 'VAM_PBMC3K_SCTransform.Rnw'

--- re-building 'VAM_pbmc_small.Rnw' using Sweave
Loading required package: MASS
Loading required package: Matrix
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
--- finished re-building 'VAM_pbmc_small.Rnw'

+-+VAM_pbmc_small.pdf

runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
--- re-building 'VAM_pbmc_small_sctransform.Rnw' using Sweave
Loading required package: MASS
Loading required package: Matrix
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
Seurat package not available! Not executing associated vignette content.
--- finished re-building 'VAM_pbmc_small_sctransform.Rnw'

+-+VAM_pbmc_small_sctransform.pdf

runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
SUMMARY: processing the following files failed:
  'VAM_pbmc_small.Rnw' 'VAM_pbmc_small_sctransform.Rnw'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING