Julian Flesch
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/waddR |
| Branch: RELEASE_3_12 |
| Last Commit: 8e4b97d |
| Last Changed Date: 2020-10-27 11:50:33 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:34:11 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the waddR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1948/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| waddR 1.4.0 (landing page) Julian Flesch
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: waddR |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:waddR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings waddR_1.4.0.tar.gz |
| StartedAt: 2021-05-06 07:55:31 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 08:01:49 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 378.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: waddR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:waddR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings waddR_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/waddR.Rcheck'
* using R version 4.0.5 (2021-03-31)
* 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 '1.4.0'
* 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
* 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 use of PKG_*FLAGS in Makefiles ... 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-3.12-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-3.12-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 (user + system) or elapsed time > 5s
user system elapsed
wasserstein.test 6.2 0.77 6.97
testZeroes-method 1.5 0.02 15.14
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wasserstein.test 5.03 0.22 5.25
testZeroes-method 1.56 0.00 13.74
* 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-3.12-bioc/meat/waddR.Rcheck/00check.log'
for details.
waddR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/waddR_1.4.0.tar.gz && rm -rf waddR.buildbin-libdir && mkdir waddR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=waddR.buildbin-libdir waddR_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL waddR_1.4.0.zip && rm waddR_1.4.0.tar.gz waddR_1.4.0.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 44406 100 44406 0 0 2943k 0 --:--:-- --:--:-- --:--:-- 3097k
install for i386
* installing *source* package 'waddR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/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:348:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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]
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 'unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
~^~~~~~~~~
wasserstein.cpp:1095:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:720:49: required from here
wasserstein.cpp:439:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:782:44: required from here
wasserstein.cpp:121:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:890:17: required from here
wasserstein.cpp:472:47: warning: comparison of integer expressions of different signedness: 'const int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:918:62: required from here
wasserstein.cpp:101:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:939:15: required from here
wasserstein.cpp:53:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:1052:15: required from here
wasserstein.cpp:169:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
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:1168:27: required from here
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
T max_x = x_sorted[n-1];
^~~~~
C:/rtools40/mingw32/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-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/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:348:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
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]
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 long unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for (int i=0; i<x.size(); i++) { x[i] = x_[i];}
~^~~~~~~~~
wasserstein.cpp:1095:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
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:720:49: required from here
wasserstein.cpp:439:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
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:782:44: 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]
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:890:17: 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 long unsigned int'} [-Wsign-compare]
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:918:62: 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]
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:939:15: required from here
wasserstein.cpp:53:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
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:1052:15: 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]
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:1168:27: required from here
wasserstein.cpp:501:4: warning: unused variable 'max_x' [-Wunused-variable]
T max_x = x_sorted[n-1];
^~~~~
C:/rtools40/mingw64/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-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/waddR.buildbin-libdir/waddR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'waddR' as waddR_1.4.0.zip
* DONE (waddR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'waddR' successfully unpacked and MD5 sums checked
|
waddR.Rcheck/tests_i386/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
+
+ })
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 92 ]
>
>
>
> proc.time()
user system elapsed
24.18 1.06 25.28
|
waddR.Rcheck/tests_x64/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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 ]
>
>
>
> proc.time()
user system elapsed
28.68 0.79 29.73
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waddR.Rcheck/examples_i386/waddR-Ex.timings
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waddR.Rcheck/examples_x64/waddR-Ex.timings
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