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### Running command:
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###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:waddR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings waddR_1.10.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/waddR.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'waddR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'waddR' version '1.10.0'
* 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 'waddR' 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 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 ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/waddR/libs/x64/waddR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'waddR-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: wasserstein.sc
> ### Title: Two-sample semi-parametric test for single-cell RNA-sequencing
> ###   data to check for differences between two distributions using the
> ###   2-Wasserstein distance
> ### Aliases: wasserstein.sc wasserstein.sc,matrix,vector-method
> ###   wasserstein.sc-method,matrix,vector,ANY,ANY,ANY-method
> ###   wasserstein.sc,SingleCellExperiment,SingleCellExperiment-method
> ###   wasserstein.sc,SingleCellExperiment,SingleCellExperiment,ANY,ANY,ANY-method
> 
> ### ** Examples
> 
> #simulate scRNA-seq data
> set.seed(24)
> nb.sim1<-rnbinom(n=(750*250),1,0.7)
> dat1<-matrix(data=nb.sim1,nrow=750,ncol=250)
> nb.sim2a<-rnbinom(n=(250*100),1,0.7)
> dat2a<-matrix(data=nb.sim2a,nrow=250,ncol=100)
> nb.sim2b<-rnbinom(n=(250*150),5,0.2)
> dat2b<-matrix(data=nb.sim2b,nrow=250,ncol=150)
> dat2<-cbind(dat2a,dat2b)
> dat<-rbind(dat1,dat2)*0.25
> #randomly shuffle the rows of the matrix to create the input matrix
> set.seed(32)
> dat<-dat[sample(nrow(dat)),]
> condition<-c(rep("A",100),rep("B",150))  
> 
> #call wasserstein.sc with a matrix and a vector including conditions
> #set seed for reproducibility
> #two-stage method
> wasserstein.sc(dat,condition,method="TS",permnum=10000,seed=24)
Error in manager$availability[[as.character(result$node)]] <- TRUE : 
  wrong args for environment subassignment
Calls: wasserstein.sc ... .bploop_impl -> .collect_result -> .manager_recv -> .manager_recv
Error in serialize(data, node$con) : error writing to connection
Calls: wasserstein.sc ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize
Error in serialize(data, node$con) : error writing to connection
Calls: wasserstein.sc ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize
Execution halted
Error in serialize(data, node$con) : error writing to connection
Calls: <Anonymous> ... .send_to -> <Anonymous> -> sendData.SOCKnode -> serialize
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  'F:/biocbuild/bbs-3.15-bioc/meat/waddR.Rcheck/00check.log'
for details.