* using log directory ‘/srv/hornik/tmp/CRAN/MiscMetabar.Rcheck’ * using R Under development (unstable) (2024-02-08 r85876) * using platform: x86_64-pc-linux-gnu * R was compiled by Debian clang version 17.0.6 (5) Debian flang-new version 17.0.6 (5) * running under: Debian GNU/Linux trixie/sid * using session charset: UTF-8 * checking for file ‘MiscMetabar/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MiscMetabar’ version ‘0.7.4’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... [5s/9s] NOTE Maintainer: ‘Adrien Taudière ’ New submission Possibly misspelled words in DESCRIPTION: Metabarcoding (3:36) MiscMetabar (7:18, 7:205, 7:284) bioinformatic (7:255) dada (7:187) metabarcoding (7:126) phyloseq (7:177) reproducibility (7:107) Found the following (possibly) invalid URLs: URL: From: inst/doc/MiscMetabar.html Message: Empty URL Found the following (possibly) invalid file URI: URI: code_of_conduct.md From: README.md * 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 whether package ‘MiscMetabar’ can be installed ... [26s/26s] OK * 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 ... [7s/7s] OK * checking whether the package can be loaded with stated dependencies ... [7s/7s] OK * checking whether the package can be unloaded cleanly ... [7s/7s] OK * checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK * checking whether the namespace can be unloaded cleanly ... [7s/7s] OK * checking loading without being on the library search path ... [7s/7s] 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 ... [35s/35s] 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 ... [4s/4s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... [193s/194s] NOTE Examples with CPU (user + system) or elapsed time > 5s user system elapsed ancombc_pq 11.439 0.428 11.868 ggbetween_pq 6.046 0.372 6.418 adonis_pq 6.183 0.044 6.227 multitax_bar_pq 5.364 0.180 5.544 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... [735s/401s] ERROR Running ‘testthat.R’ [735s/401s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(MiscMetabar) Loading required package: phyloseq Loading required package: ggplot2 Loading required package: dada2 Loading required package: Rcpp Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:testthat': matches The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union > > test_check("MiscMetabar") Starting 2 test processes ✔ Updated metadata database: 2.88 MB in 8 files. ℹ Updating metadata database ✔ Updating metadata database ... done → Will install 2 packages. → Will download 2 CRAN packages (5.76 MB). + abc 2.2.1 [bld][dl] (869.83 kB) + abc.data 1.0 [bld][dl] (4.89 MB) ℹ Getting 2 pkgs (5.76 MB) ✔ Got abc 2.2.1 (source) (869.83 kB) ✔ Got abc.data 1.0 (source) (4.89 MB) ℹ Building abc.data 1.0 ✔ Built abc.data 1.0 (841ms) ✔ Installed abc.data 1.0 (1s) ℹ Building abc 2.2.1 ✔ Built abc 2.2.1 (3.3s) ✔ Installed abc 2.2.1 (1s) ✔ 1 pkg + 10 deps: kept 9, added 2, dld 2 (5.76 MB) [20.7s] [ FAIL 3 | WARN 1 | SKIP 2 | PASS 507 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test_misc.R:103:3', 'test_figures_taxo.R:354:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_cutadapt.R:17:5'): cutadapt_remove_primers works fine ──────── length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`). `actual`: 0 `expected`: 2 ── Failure ('test_cutadapt.R:37:5'): cutadapt_remove_primers works fine ──────── length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`). `actual`: 0 `expected`: 2 ── Failure ('test_cutadapt.R:55:5'): cutadapt_remove_primers works fine ──────── length(list.files(paste0(tempdir(), "/output_cutadapt"))) (`actual`) not equal to 2 (`expected`). `actual`: 0 `expected`: 2 [ FAIL 3 | WARN 1 | SKIP 2 | PASS 507 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [12s/12s] OK * checking PDF version of manual ... [5s/5s] OK * checking HTML version of manual ... [2s/2s] 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