* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/metacoder.Rcheck’ * using R Under development (unstable) (2024-08-23 r87049) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc-14 (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Fedora Linux 36 (Workstation Edition) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘metacoder/DESCRIPTION’ ... OK * this is package ‘metacoder’ version ‘0.3.7’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Package suggested but not available for checking: ‘traits’ * 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 whether package ‘metacoder’ can be installed ... [63s/96s] OK * used C++ compiler: ‘g++-14 (GCC) 14.2.0’ * 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 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 use of S3 registration ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘R6’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [35s/71s] OK * checking Rd files ... 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 ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 ... [18s/25s] OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [62s/70s] [63s/71s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > > suppressPackageStartupMessages(library(metacoder)) > > test_check("metacoder") [ FAIL 1 | WARN 0 | SKIP 4 | PASS 532 ] ══ Skipped tests (4) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test--parsers_and_writers.R:201:3', 'test--simulated_pcr.R:19:3', 'test--taxmap_parsers.R:139:3', 'test--taxmap_parsers.R:288:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test--parsers_and_writers.R:104:3'): Newick parsing ───────────────── Error: Please install phylotate Backtrace: ▆ 1. └─metacoder::parse_newick("example_data/newick_example_1.txt") at test--parsers_and_writers.R:104:3 2. └─metacoder:::check_for_pkg("phylotate") [ FAIL 1 | WARN 0 | SKIP 4 | PASS 532 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... [28s/35s] OK * checking HTML version of manual ... [14s/22s] 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 See ‘/data/gannet/ripley/R/packages/tests-Suggests/metacoder.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 7:43.96, 287.29 + 19.40