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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:waddR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings waddR_1.21.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/waddR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waddR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘waddR’ version ‘1.21.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 for sufficient/correct file permissions ... OK
* checking whether package ‘waddR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 is not available
* 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)
Warning in parallel::mccollect(wait = FALSE, timeout = 1) :
  1 parallel job did not deliver a result
Error in reducer$value.cache[[as.character(idx)]] <- values : 
  wrong args for environment subassignment
Calls: wasserstein.sc ... .bploop_impl -> .collect_result -> .reducer_add -> .reducer_add
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
testZeroes-method 5.937  1.149   2.786
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  +   test_check("waddR")
  + 
  + })
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 91 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_wasserstein_sc.r:165:5'): Correctness of wasserstein single cell output ──
  res.os.3[os.volatile.fields] not equal to res.os.values.3[os.volatile.fields].
  2/2 mismatches (average diff: NaN)
  [1] NaN - 0 == NaN
  [2] NaN - 0 == NaN
  
  [ FAIL 1 | WARN 3 | SKIP 0 | PASS 91 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/waddR.Rcheck/00check.log’
for details.