##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:waddR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings waddR_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/waddR.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'waddR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'waddR' version '1.13.0'
* 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
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* 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-3.17-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 nor [v]sprintf. 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-3.17-bioc-rtools43/meat/waddR.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL waddR
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'waddR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.17-bioc/R/library/RcppArmadillo/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c wasserstein.cpp -o wasserstein.o
wasserstein.cpp: In function 'std::vector<double> rep_weighted(std::vector<double>, std::vector<int, std::allocator<int> >)':
wasserstein.cpp:348:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  348 |         for(int i=0; i<x.size(); i++) {
      |                      ~^~~~~~~~~
wasserstein.cpp: In function 'std::vector<double> concat(std::vector<double>&, std::vector<double>&)':
wasserstein.cpp:386:34: warning: variable 'out_it_end' set but not used [-Wunused-but-set-variable]
  386 |         vector<double>::iterator out_it_end = out.end();
      |                                  ^~~~~~~~~~
wasserstein.cpp: In function 'std::vector<int, std::allocator<int> > interval_table(const std::vector<double>&, const std::vector<double>&, int)':
wasserstein.cpp:584:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  584 |                         while (data_i < datavec.size()) {
      |                                ~~~~~~~^~~~~~~~~~~~~~~~
wasserstein.cpp: In function 'double cor_test_export(Rcpp::NumericVector, Rcpp::NumericVector)':
wasserstein.cpp:1088:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1088 |         for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
      |                       ~^~~~~~~~~
wasserstein.cpp:1089:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
 1089 |         for (int j=0; j<y.size(); j++) { y[j] = y_[j];}
      |                       ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'double cor(const std::vector<T>&, const std::vector<T>&, double, double) [with T = double]':
wasserstein.cpp:716:24:   required from here
wasserstein.cpp:439:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  439 |         for (int i=0; i<x.size(); i++){
      |                       ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> operator-(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:778:44:   required from here
wasserstein.cpp:121:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  121 |     for (int i=0; i<x.size(); i++) {
      |                   ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> cumSum(const std::vector<T>&, int) [with T = double]':
wasserstein.cpp:884:14:   required from here
wasserstein.cpp:472:54: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  472 |         int upper = ((last_index > 0) && (last_index <= x.size())
      |                                          ~~~~~~~~~~~~^~~~~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> operator*(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:912:62:   required from here
wasserstein.cpp:101:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  101 |     for (int i=0; i<x.size(); i++) {
      |                   ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> operator+(std::vector<T>, std::vector<T>) [with T = double]':
wasserstein.cpp:933:15:   required from here
wasserstein.cpp:53:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
   53 |                 for (int i=0; i<x.size(); i++) {
      |                               ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> operator/(const std::vector<T>&, const std::vector<T>&) [with T = double]':
wasserstein.cpp:1046:15:   required from here
wasserstein.cpp:169:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  169 |     for (int i=0; i<x.size(); i++) {
      |                   ~^~~~~~~~~
wasserstein.cpp: In instantiation of 'std::vector<T> quantile(const std::vector<T>&, std::vector<double>, int) [with T = double]':
wasserstein.cpp:1162:16:   required from here
wasserstein.cpp:501:11: warning: unused variable 'max_x' [-Wunused-variable]
  501 |         T max_x = x_sorted[n-1];
      |           ^~~~~
g++ -shared -s -static-libgcc -o waddR.dll tmp.def RcppExports.o wasserstein.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-waddR/00new/waddR/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (waddR)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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 0 | WARN 3 | SKIP 0 | PASS 92 ]

[ FAIL 0 | WARN 3 | SKIP 0 | PASS 92 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
  24.56    0.95  236.37