* using log directory ‘/srv/hornik/tmp/CRAN/warbleR.Rcheck’ * using R Under development (unstable) (2023-08-31 r85038) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 16.0.6 (10) GNU Fortran (Debian 13.2.0-1) 13.2.0 * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘warbleR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘warbleR’ version ‘1.1.29’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [6s/8s] NOTE Maintainer: ‘Marcelo Araya-Salas ’ Found the following (possibly) invalid URLs: URL: https://marce10.github.io/2016/09/12/Similarity_of_acoustic_signals_with_dynamic_time_warping_(DTW).html From: inst/doc/warbleR_workflow_03.html Status: 404 Message: Not Found URL: https://marce10.github.io/2017/02/17/Choosing_the_right_method_for_measuring_acoustic_signal_structure.html From: inst/doc/warbleR_workflow_03.html Status: 404 Message: Not Found URL: https://marce10.github.io/2017/03/17/Creating_song_catalogs.html From: inst/doc/warbleR_workflow_02.html Status: 404 Message: Not Found URL: https://marce10.github.io/2017/07/31/Updates_on_catalog_function.html From: inst/doc/warbleR_workflow_02.html Status: 404 Message: Not Found URL: https://marce10.github.io/warbleR/reference/harmonic_track.html From: inst/doc/Intro_to_warbleR.html Status: 404 Message: Not Found URL: https://marce10.github.io/warbleR/reference/optimize_auto_detec.html From: inst/doc/Intro_to_warbleR.html Status: 404 Message: Not Found URL: https://marce10.github.io/warbleR/reference/track_freqs.html From: inst/doc/Intro_to_warbleR.html Status: 404 Message: Not Found GNU make is a SystemRequirements. * 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 executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking serialization versions ... OK * checking whether package ‘warbleR’ can be installed ... [18s/18s] OK * used C++ compiler: ‘Debian clang version 16.0.6 (11)’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking package directory ... OK * checking for future file timestamps ... 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 ... [1s/1s] OK * checking whether the package can be loaded with stated dependencies ... [1s/1s] OK * checking whether the package can be unloaded cleanly ... [1s/1s] OK * checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK * checking whether the namespace can be unloaded cleanly ... [1s/1s] OK * checking loading without being on the library search path ... [1s/1s] OK * checking whether startup messages can be suppressed ... [1s/1s] OK * checking use of S3 registration ... 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 ... [29s/29s] OK * checking Rd files ... [1s/1s] OK * checking Rd metadata ... OK * checking Rd line widths ... 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... [0s/0s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [17s/17s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [29s/32s] ERROR Running ‘testthat.R’ [28s/32s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(warbleR) Loading required package: tuneR Loading required package: seewave Loading required package: NatureSounds Loading required package: knitr > > test_check("warbleR") sound.files duration org.selec selec start end 1 Phae.long1.wav NA 1 NA NA NA 2 Phae.long1.wav NA 2 NA NA NA 3 Phae.long2.wav NA 3 NA NA NA 4 Phae.long2.wav NA 4 NA NA NA Time range: 0.265s; frequency range: 1-10 kHz Time range: 0.215s; frequency range: 1-10 kHz all selections are OK measuring dominant frequency contours (step 1 of 3): Measuring fundamental frequency: measuring spectral parameters (step 2 of 3): creating image files (step 3 of 3): measuring spectral parameters (step 1 of 3): measuring spectral parameters + harmonicity (step 2 of 3): creating image files (step 3 of 3): measuring fundamental frequency contours (step 1 of 3): Measuring fundamental frequency: measuring mel frequency cepstral coefficients (step 2 of 3): creating image files (step 3 of 3): creating spectrogram matrices (step 1 of 4): running cross-correlation (step 2 of 4): measuring mel frequency cepstral coefficients (step 3 of 4): creating image files (step 4 of 4): 4 files were found Collecting file metadata (can take some time) sh: 1: sox: not found 16 recording(s) found! sh: 1: sox: not found Object of class 'selection_table' * The output of the following call: selection_table(X = lbh_selec_table[1:3, ], path = tempdir(), pb = FALSE) Contains: * A selection table data frame with 3 rows and 7 columns: |sound.files | channel| selec| start| end| bottom.freq| |:--------------|-------:|-----:|------:|------:|-----------:| |Phae.long1.wav | 1| 1| 1.1694| 1.3424| 2.2201| |Phae.long1.wav | 1| 2| 2.1584| 2.3215| 2.1694| |Phae.long1.wav | 1| 3| 0.3433| 0.5183| 2.2183| ... 1 more column(s) (top.freq) * A data frame (check.results) generated by check_sels() (as attribute) created by warbleR 1.1.29 Object of class 'extended_selection_table' * The output of the following call: selection_table(X = lbh_selec_table[1:3, ], path = tempdir(), extended = TRUE, confirm.extended = FALSE, pb = FALSE) Contains: * A selection table data frame with 3 row(s) and 7 columns: |sound.files | channel| selec| start| end| bottom.freq| |:----------------|-------:|-----:|-----:|------:|-----------:| |Phae.long1.wav_1 | 1| 1| 0.1| 0.2730| 2.2201| |Phae.long1.wav_2 | 1| 1| 0.1| 0.2630| 2.1694| |Phae.long1.wav_3 | 1| 1| 0.1| 0.2749| 2.2183| ... 1 more column(s) (top.freq) * 3 wave object(s) (as attributes): Phae.long1.wav_1Phae.long1.wav_2Phae.long1.wav_3 * A data frame (check.results) generated by check_sels() (as attribute) The selection table was created by element (see 'class_extended_selection_table') * 1 sampling rate(s) (in kHz): 22.5 * 1 bit depth(s): 16 * Created by warbleR 1.1.29 Time range: 0.373s; frequency range: 0-10 kHz 16 recording(s) found! [ FAIL 3 | WARN 1 | SKIP 0 | PASS 68 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-fix_wavs.R:15:5'): basic ─────────────────────────────────────── Error in `system(cll, ignore.stdout = FALSE, intern = TRUE)`: error in running command Backtrace: ▆ 1. └─warbleR::fix_wavs(...) at test-fix_wavs.R:15:4 2. └─warbleR:::pblapply_wrblr_int(pbar = TRUE, X = fls, FUN = fix_sox_FUN) 3. └─base::lapply(X[Split[[i]]], FUN, ...) 4. └─warbleR (local) FUN(X[[i]], ...) 5. └─base::system(cll, ignore.stdout = FALSE, intern = TRUE) ── Error ('test-mp32wav.R:9:3'): basic ───────────────────────────────────────── Error: Sox is not installed or is not available in path Backtrace: ▆ 1. └─warbleR::mp32wav(...) at test-mp32wav.R:9:2 2. └─warbleR:::stop2("Sox is not installed or is not available in path") ── Error ('test-resample_est.R:18:3'): basic ─────────────────────────────────── Error in `system(cll, ignore.stdout = FALSE, intern = TRUE)`: error in running command Backtrace: ▆ 1. └─warbleR::resample_est(X, pb = FALSE) at test-resample_est.R:18:2 2. └─warbleR:::pblapply_wrblr_int(...) 3. └─base::lapply(X, FUN, ...) 4. └─warbleR (local) FUN(X[[i]], ...) 5. ├─base::suppressWarnings(system(cll, ignore.stdout = FALSE, intern = TRUE)) 6. │ └─base::withCallingHandlers(...) 7. └─base::system(cll, ignore.stdout = FALSE, intern = TRUE) [ FAIL 3 | WARN 1 | SKIP 0 | PASS 68 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking re-building of vignette outputs ... [8s/8s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [3s/3s] OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 1 ERROR, 2 NOTEs