* using log directory 'd:/Rcompile/CRANpkg/local/3.6/ClustAssess.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 'ClustAssess/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClustAssess' version '0.1.1'
* 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 'ClustAssess' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... [8s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compiled code ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'ClustAssess-Ex.R' failed
The error most likely occurred in:

> ### Name: marker_overlap
> ### Title: Cell-wise marker gene overlap
> ### Aliases: marker_overlap
> 
> ### ** Examples
> 
> suppressWarnings({
+ set.seed(12345)
+ library(Seurat)
+ 
+ # cluster with Louvain algorithm
+ pbmc_small = FindClusters(pbmc_small, resolution=0.8, verbose=FALSE)
+ 
+ # cluster with k-means
+ pbmc.pca = Embeddings(pbmc_small, 'pca')
+ pbmc_small@meta.data$kmeans_clusters = kmeans(pbmc.pca, centers=2)$cluster
+ 
+ # compare the markers
+ Idents(pbmc_small) = pbmc_small@meta.data$seurat_clusters
+ louvain.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ Idents(pbmc_small) = pbmc_small@meta.data$kmeans_clusters
+ kmeans.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ pbmc_small@meta.data$jsi = marker_overlap(louvain.markers, kmeans.markers,
+   pbmc_small@meta.data$seurat_clusters, pbmc_small@meta.data$kmeans_clusters)
+ 
+ # which cells have the same markers, regardless of clustering?
+ FeaturePlot(pbmc_small, 'jsi')
+ })
Error: package or namespace load failed for 'Seurat':
 object 'markvario' is not exported by 'namespace:spatstat'
Execution halted

runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
** running examples for arch 'x64' ... ERROR
Running examples in 'ClustAssess-Ex.R' failed
The error most likely occurred in:

> ### Name: marker_overlap
> ### Title: Cell-wise marker gene overlap
> ### Aliases: marker_overlap
> 
> ### ** Examples
> 
> suppressWarnings({
+ set.seed(12345)
+ library(Seurat)
+ 
+ # cluster with Louvain algorithm
+ pbmc_small = FindClusters(pbmc_small, resolution=0.8, verbose=FALSE)
+ 
+ # cluster with k-means
+ pbmc.pca = Embeddings(pbmc_small, 'pca')
+ pbmc_small@meta.data$kmeans_clusters = kmeans(pbmc.pca, centers=2)$cluster
+ 
+ # compare the markers
+ Idents(pbmc_small) = pbmc_small@meta.data$seurat_clusters
+ louvain.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ Idents(pbmc_small) = pbmc_small@meta.data$kmeans_clusters
+ kmeans.markers = FindAllMarkers(pbmc_small, logfc.threshold=1, verbose=FALSE)
+ 
+ pbmc_small@meta.data$jsi = marker_overlap(louvain.markers, kmeans.markers,
+   pbmc_small@meta.data$seurat_clusters, pbmc_small@meta.data$kmeans_clusters)
+ 
+ # which cells have the same markers, regardless of clustering?
+ FeaturePlot(pbmc_small, 'jsi')
+ })
Error: package or namespace load failed for 'Seurat':
 object 'markvario' is not exported by 'namespace:spatstat'
Execution halted

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 ... [20s] WARNING
Error(s) in re-building vignettes:
--- re-building 'ClustAssess.Rmd' using rmarkdown
Quitting from lines 22-27 (ClustAssess.Rmd) 
Error: processing vignette 'ClustAssess.Rmd' failed with diagnostics:
package or namespace load failed for 'Seurat':
 object 'markvario' is not exported by 'namespace:spatstat'
--- failed re-building 'ClustAssess.Rmd'


runtime error R6031
- Attempt to initialize the CRT more than once.
This indicates a bug in your application.
--- re-building 'comparing-soft-and-hierarchical.Rmd' using rmarkdown
--- finished re-building 'comparing-soft-and-hierarchical.Rmd'

SUMMARY: processing the following file failed:
  'ClustAssess.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING