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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:waddR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings waddR_1.6.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/waddR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.6.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘waddR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: DEPRECATION: As of BiocFileCache (>1.15.1), default caching location has changed.
See ‘/Users/biocbuild/bbs-3.13-bioc/meat/waddR.Rcheck/00install.out’ for details.
* 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 ... NOTE
Warning: DEPRECATION: As of BiocFileCache (>1.15.1), default caching location has changed.
  Problematic cache: /Users/biocbuild/Library/Caches/BiocFileCache
  See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update


A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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 2886.407 109.948 756.650
testZeroes-method       57.274   8.594  18.804
* 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 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/waddR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL waddR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘waddR’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/RcppArmadillo/include' -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o waddR.so RcppExports.o wasserstein.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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
Warning: DEPRECATION: As of BiocFileCache (>1.15.1), default caching location has changed.
  Problematic cache: /Users/biocbuild/Library/Caches/BiocFileCache
  See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update

** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: DEPRECATION: As of BiocFileCache (>1.15.1), default caching location has changed.
  Problematic cache: /Users/biocbuild/Library/Caches/BiocFileCache
  See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update

** testing if installed package keeps a record of temporary installation path
* DONE (waddR)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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)
Warning message:
DEPRECATION: As of BiocFileCache (>1.15.1), default caching location has changed.
  Problematic cache: /Users/biocbuild/Library/Caches/BiocFileCache
  See https://www.bioconductor.org/packages/devel/bioc/vignettes/BiocFileCache/inst/doc/BiocFileCache.html#default-caching-location-update
 
> 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 
 19.739   0.725  20.455