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###
### Running command:
###
###   /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_1.22.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/waddR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waddR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘waddR’ version ‘1.22.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘waddR’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* 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 21.184  3.564   9.887
* 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:
    8.       ├─BiocParallel::bpmapply(...)
    9.       └─BiocParallel::bpmapply(...)
   10.         ├─BiocParallel::bplapply(...)
   11.         └─BiocParallel::bplapply(...)
   12.           └─BiocParallel:::.bpinit(...)
   13.             ├─BiocParallel::bploop(...)
   14.             └─BiocParallel:::bploop.lapply(...)
   15.               └─BiocParallel:::.bploop_impl(...)
   16.                 └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
   17.                   ├─BiocParallel:::.reducer_add(reducer, njob, value)
   18.                   └─BiocParallel:::.reducer_add(reducer, njob, value)
  
  [ FAIL 1 | WARN 4 | SKIP 0 | PASS 76 ]
  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.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL waddR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘waddR’ ...
** this is package ‘waddR’ version ‘1.22.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c wasserstein.cpp -o wasserstein.o
wasserstein.cpp:386:27: warning: unused variable 'out_it_end' [-Wunused-variable]
        vector<double>::iterator out_it_end = out.end();
                                 ^
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
        T max_x = x_sorted[n-1];
          ^
wasserstein.cpp:1162:8: note: in instantiation of function template specialization 'quantile<double>' requested here
        res = quantile(x, q, type);
              ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o waddR.so RcppExports.o wasserstein.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-waddR/00new/waddR/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (waddR)

R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(waddR)
> library(devtools)
Loading required package: usethis

Attaching package: 'devtools'

The following object is masked from 'package:testthat':

    test_file

> library(rprojroot)
> 
> # Workaround for issue on build systems, where package directory can't be found
> # and tests for non-exported functions throw errors.
> tryCatch({
+ 
+   dir.start <- "."
+   if ("waddR" %in% dir(".."))
+     dir.start <- "../waddR/"
+   crit <- has_dir("DESCRIPTION")
+   abspath <- find_root(dir.start, criterion=crit)
+   #load the non-exported functions defined in waddR
+   load_all(abspath)
+       
+ }, error = function(err){
+ 
+   # Workaround of finding the package dir has not worked => catch 
+   # rprojroot::find_root() error. Redefine all non-exported functions that are
+   # tested as a dummy function to avaid "not defined" errors and have them 
+   # skipped
+   dummy <- function(...) {return(1)}
+   abs_test_export <- dummy
+   sum_test_export <- dummy
+   mean_test_export <- dummy
+   sd_test_export <- dummy
+   subtract_test_export <- dummy
+   add_test_export <- dummy
+   add_test_export_sv <- dummy
+   divide_test_export_vectors <- dummy
+   divide_test_export_sv <- dummy
+   multiply_test_export_sv <- dummy
+   multiply_test_export <- dummy
+   pow_test_export <- dummy
+   cumSum_test_export <- dummy
+   interval_table_test_export <- dummy
+   rep_weighted_test_export <- dummy
+   concat_test_export <- dummy
+   cor_test_export <- dummy
+   equidist_quantile_test_export <- dummy
+   quantile_test_export <- dummy
+ 
+ }, finally = {
+ 
+   # run tests:
+   #   A) on all functions, both exported and non-exported
+   #   B) just on exported, skip all non-exported
+   test_check("waddR")
+ 
+ })
[ FAIL 1 | WARN 4 | SKIP 0 | PASS 76 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_wasserstein_sc.r:106:5'): Correctness of wasserstein single cell output ──
Error in `reducer$value.cache[[as.character(idx)]] <- values`: wrong args for environment subassignment
Backtrace:
     ▆
  1. ├─waddR::wasserstein.sc(dat, condition1, "OS") at test_wasserstein_sc.r:106:5
  2. └─waddR::wasserstein.sc(dat, condition1, "OS")
  3.   └─waddR:::.testWass(x, y, permnum, inclZero = TRUE, seed = seed)
  4.     ├─base::t(...)
  5.     ├─base::simplify2array(...)
  6.     ├─BiocParallel::bpmapply(onegene, seq(ngenes))
  7.     └─BiocParallel::bpmapply(onegene, seq(ngenes))
  8.       ├─BiocParallel::bpmapply(...)
  9.       └─BiocParallel::bpmapply(...)
 10.         ├─BiocParallel::bplapply(...)
 11.         └─BiocParallel::bplapply(...)
 12.           └─BiocParallel:::.bpinit(...)
 13.             ├─BiocParallel::bploop(...)
 14.             └─BiocParallel:::bploop.lapply(...)
 15.               └─BiocParallel:::.bploop_impl(...)
 16.                 └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
 17.                   ├─BiocParallel:::.reducer_add(reducer, njob, value)
 18.                   └─BiocParallel:::.reducer_add(reducer, njob, value)

[ FAIL 1 | WARN 4 | SKIP 0 | PASS 76 ]
Error: Test failures
Execution halted