Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:41 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2227/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
waddR 1.19.0 (landing page) Julian Flesch
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the waddR package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: waddR |
Version: 1.19.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:waddR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings waddR_1.19.0.tar.gz |
StartedAt: 2024-08-27 05:04:33 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 05:18:33 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 840.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: waddR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:waddR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings waddR_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/waddR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘waddR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘waddR’ version ‘1.19.0’ * 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ * 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 1991.118 47.457 516.774 testZeroes-method 18.688 1.810 7.628 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/waddR.Rcheck/00check.log’ for details.
waddR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL waddR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘waddR’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-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:348:23: 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 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 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 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 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:53:32: 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 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 wasserstein.cpp:501:11: warning: unused variable ‘max_x’ [-Wunused-variable] 501 | T max_x = x_sorted[n-1]; | ^~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o waddR.so RcppExports.o wasserstein.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/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)
waddR.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-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. 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 ] [ FAIL 0 | WARN 3 | SKIP 0 | PASS 92 ] > > > > proc.time() user system elapsed 20.132 2.675 22.233
waddR.Rcheck/waddR-Ex.timings
name | user | system | elapsed | |
permutations | 0 | 0 | 0 | |
squared_wass_approx | 0 | 0 | 0 | |
squared_wass_decomp | 0.001 | 0.001 | 0.001 | |
testZeroes-method | 18.688 | 1.810 | 7.628 | |
wasserstein.sc-method | 1991.118 | 47.457 | 516.774 | |
wasserstein.test | 3.192 | 0.836 | 4.028 | |
wasserstein_metric | 0 | 0 | 0 | |