Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:09:00 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the waddR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]:packages/waddR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 2058/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
waddR 1.8.0 (landing page) Julian Flesch
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: waddR |
Version: 1.8.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:waddR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings waddR_1.8.0.tar.gz |
StartedAt: 2022-04-12 19:56:42 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 20:14:59 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 1096.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: waddR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:waddR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings waddR_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/waddR.Rcheck’ * using R version 4.1.3 (2022-03-10) * 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 ‘1.8.0’ * 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 2864.262 117.299 777.638 testZeroes-method 63.004 9.384 21.040 * 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 ‘/Users/biocbuild/bbs-3.14-bioc/meat/waddR.Rcheck/00check.log’ for details.
waddR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL waddR ### ############################################################################## ############################################################################## * 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 ** 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 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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) > 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 21.777 3.152 24.794
waddR.Rcheck/waddR-Ex.timings
name | user | system | elapsed | |
permutations | 0.000 | 0.001 | 0.002 | |
squared_wass_approx | 0.001 | 0.001 | 0.003 | |
squared_wass_decomp | 0.001 | 0.001 | 0.003 | |
testZeroes-method | 63.004 | 9.384 | 21.040 | |
wasserstein.sc-method | 2864.262 | 117.299 | 777.638 | |
wasserstein.test | 3.412 | 0.275 | 3.687 | |
wasserstein_metric | 0.001 | 0.000 | 0.001 | |