Package: waddR

Version: 1.0.1

Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:waddR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings waddR_1.0.1.tar.gz

StartedAt: 2020-04-15 07:24:34 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:30:23 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 348.8 seconds

RetCode: 0

Status:  OK

CheckDir: waddR.Rcheck

Warnings: 0

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:waddR.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings waddR_1.0.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/waddR.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'waddR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'waddR' version '1.0.1'
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/waddR/libs/i386/waddR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/waddR/libs/x64/waddR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
wasserstein.test  5.90   0.60     6.5
testZeroes-method 1.15   0.01    13.8
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
wasserstein.test  6.89   0.19    7.08
testZeroes-method 1.68   0.04   15.97
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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 NOTE
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/waddR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/waddR_1.0.1.tar.gz && rm -rf waddR.buildbin-libdir && mkdir waddR.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=waddR.buildbin-libdir waddR_1.0.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL waddR_1.0.1.zip && rm waddR_1.0.1.tar.gz waddR_1.0.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 44448  100 44448    0     0   502k      0 --:--:-- --:--:-- --:--:--  529k

install for i386

* installing *source* package 'waddR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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:348:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In function 'std::vector<int, std::allocator<int> > interval_table(const std::vector<double>&, const std::vector<double>&, int)':
wasserstein.cpp:584:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while (data_i < datavec.size()) {
                  ^
wasserstein.cpp: In function 'double cor_test_export(Rcpp::NumericVector, Rcpp::NumericVector)':
wasserstein.cpp:1094:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
                 ^
wasserstein.cpp:1095:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int j=0; j<y.size(); j++) { y[j] = y_[j];}
                 ^
wasserstein.cpp: In instantiation of 'double cor(const std::vector<_RealType>&, const std::vector<_RealType>&, double, double) [with T = double]':
wasserstein.cpp:720:49:   required from here
wasserstein.cpp:439:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<x.size(); i++){
                 ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator-(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:782:44:   required from here
wasserstein.cpp:121:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> cumSum(const std::vector<_RealType>&, int) [with T = double]':
wasserstein.cpp:890:17:   required from here
wasserstein.cpp:472:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  int upper = ((last_index > 0) && (last_index <= x.size()) 
                                               ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator*(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:918:62:   required from here
wasserstein.cpp:101:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator+(std::vector<_RealType>, std::vector<_RealType>) [with T = double]':
wasserstein.cpp:939:15:   required from here
wasserstein.cpp:53:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<x.size(); i++) {
                  ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator/(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:1052:15:   required from here
wasserstein.cpp:169:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> quantile(const std::vector<_RealType>&, std::vector<double>, int) [with T = double]':
wasserstein.cpp:1168:27:   required from here
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
  T max_x = x_sorted[n-1];
    ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o waddR.dll tmp.def RcppExports.o wasserstein.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/waddR.buildbin-libdir/00LOCK-waddR/00new/waddR/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'waddR'
    finding HTML links ... done
    brownianBridgeEmpcdf.url                html  
    dot-brownianBridgeEmpcdf                html  
    dot-combinePVal                         html  
    dot-fishersCombinedPval                 html  
    dot-quantileCorrelation                 html  
    dot-relativeError                       html  
    dot-testWass                            html  
    dot-wassPermProcedure                   html  
    dot-wassersteinTestAsy                  html  
    dot-wassersteinTestSp                   html  
    permutations                            html  
    squared_wass_approx                     html  
    squared_wass_decomp                     html  
    testZeroes-method                       html  
    waddR-package                           html  
    wasserstein.sc-method                   html  
    wasserstein.test                        html  
    wasserstein_metric                      html  
** 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

install for x64

* installing *source* package 'waddR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -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:348:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for(int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In function 'std::vector<int, std::allocator<int> > interval_table(const std::vector<double>&, const std::vector<double>&, int)':
wasserstein.cpp:584:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    while (data_i < datavec.size()) {
                  ^
wasserstein.cpp: In function 'double cor_test_export(Rcpp::NumericVector, Rcpp::NumericVector)':
wasserstein.cpp:1094:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
                 ^
wasserstein.cpp:1095:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int j=0; j<y.size(); j++) { y[j] = y_[j];}
                 ^
wasserstein.cpp: In instantiation of 'double cor(const std::vector<_RealType>&, const std::vector<_RealType>&, double, double) [with T = double]':
wasserstein.cpp:720:49:   required from here
wasserstein.cpp:439:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i=0; i<x.size(); i++){
                 ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator-(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:782:44:   required from here
wasserstein.cpp:121:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> cumSum(const std::vector<_RealType>&, int) [with T = double]':
wasserstein.cpp:890:17:   required from here
wasserstein.cpp:472:47: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  int upper = ((last_index > 0) && (last_index <= x.size()) 
                                               ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator*(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:918:62:   required from here
wasserstein.cpp:101:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator+(std::vector<_RealType>, std::vector<_RealType>) [with T = double]':
wasserstein.cpp:939:15:   required from here
wasserstein.cpp:53:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i=0; i<x.size(); i++) {
                  ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> operator/(const std::vector<_RealType>&, const std::vector<_RealType>&) [with T = double]':
wasserstein.cpp:1052:15:   required from here
wasserstein.cpp:169:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i=0; i<x.size(); i++) {
                    ^
wasserstein.cpp: In instantiation of 'std::vector<_RealType> quantile(const std::vector<_RealType>&, std::vector<double>, int) [with T = double]':
wasserstein.cpp:1168:27:   required from here
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
  T max_x = x_sorted[n-1];
    ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o waddR.dll tmp.def RcppExports.o wasserstein.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/waddR.buildbin-libdir/waddR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'waddR' as waddR_1.0.1.zip
* DONE (waddR)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'waddR' successfully unpacked and MD5 sums checked

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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")
+ 
+ })
== testthat results  ===========================================================
[ OK: 92 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
  23.00    1.15   24.82 

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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")
+ 
+ })
== testthat results  ===========================================================
[ OK: 92 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 0 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
  21.37    0.68   22.56