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This page was generated on 2021-11-24 15:05:19 -0500 (Wed, 24 Nov 2021).

CHECK results for waddR on nebbiolo2

To the developers/maintainers of the waddR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/waddR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2058/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
waddR 1.8.0  (landing page)
Julian Flesch
Snapshot Date: 2021-11-23 04:15:06 -0500 (Tue, 23 Nov 2021)
git_url: https://git.bioconductor.org/packages/waddR
git_branch: RELEASE_3_14
git_last_commit: 540ab09
git_last_commit_date: 2021-10-26 12:55:17 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: waddR
Version: 1.8.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:waddR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings waddR_1.8.0.tar.gz
StartedAt: 2021-11-23 11:37:18 -0500 (Tue, 23 Nov 2021)
EndedAt: 2021-11-23 11:50:28 -0500 (Tue, 23 Nov 2021)
EllapsedTime: 789.9 seconds
RetCode: 0
Status:   OK  
CheckDir: waddR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:waddR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings waddR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/waddR.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘waddR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘waddR’ version ‘1.8.0’
* 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
* 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 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 1854.063 46.714 532.481
wasserstein.test       165.846  4.988   2.336
testZeroes-method       57.844  6.688  21.197
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/waddR.Rcheck/00check.log’
for details.



Installation output

waddR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL waddR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘waddR’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 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:386:27: 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:584:18: 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:1088:17: 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:1089:17: 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:716:49:   required from here
wasserstein.cpp:439:17: 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
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:884:17:   required from here
wasserstein.cpp:472:47: 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
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
wasserstein.cpp:53:18: 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
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:1162:27:   required from here
wasserstein.cpp:501:4: warning: unused variable ‘max_x’ [-Wunused-variable]
  501 |  T max_x = x_sorted[n-1];
      |    ^~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o waddR.so RcppExports.o wasserstein.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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)

Tests output

waddR.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 ]
> 
> 
> 
> proc.time()
   user  system elapsed 
 18.113   3.413  20.921 

Example timings

waddR.Rcheck/waddR-Ex.timings

nameusersystemelapsed
permutations0.0010.0000.001
squared_wass_approx0.0010.0000.001
squared_wass_decomp000
testZeroes-method57.844 6.68821.197
wasserstein.sc-method1854.063 46.714 532.481
wasserstein.test165.846 4.988 2.336
wasserstein_metric0.0000.0000.001