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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:waddR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings waddR_1.23.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/waddR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waddR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘waddR’ version ‘1.23.0’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* 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 loading without being on the library search path ... 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
wasserstein.sc-method 2415.374 24.432 668.010
wasserstein.test       188.818  2.325   3.628
testZeroes-method       26.651  2.773  10.028
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/waddR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL waddR
###
##############################################################################
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘waddR’ ...
** this is package ‘waddR’ version ‘1.23.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c wasserstein.cpp -o wasserstein.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
                 from wasserstein.cpp:6:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
   66 |         #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
      |                                                                                                                                                                                                       ^
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 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 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 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 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
  716 |                 quantile_cor_ab = cor(quantiles_a, quantiles_b);
      |                                   ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
wasserstein.cpp:439:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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
  778 |         squared_quantile_diff = pow(quantiles_a - quantiles_b, (double) 2.0);
      |                                                   ^~~~~~~~~~~
wasserstein.cpp:121:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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
  884 |         cua = cumSum(ua);
      |               ~~~~~~^~~~
wasserstein.cpp:472:54: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<double>::size_type’ {aka ‘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
  912 |         wsum = sum((uu1 - uu0) * pow(abs(b_weighted - a_weighted), p));
      |                                                                     ^
wasserstein.cpp:101:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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
  933 |         result = x + y;
      |                      ^
wasserstein.cpp:53:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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
 1046 |         result = x / y;
      |                      ^
wasserstein.cpp:169:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘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
 1162 |         res = quantile(x, q, type);
      |               ~~~~~~~~^~~~~~~~~~~~
wasserstein.cpp:501:11: warning: unused variable ‘max_x’ [-Wunused-variable]
  501 |         T max_x = x_sorted[n-1];
      |           ^~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o waddR.so RcppExports.o wasserstein.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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.

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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 
 23.857   3.071  26.417