• using R Under development (unstable) (2025-09-14 r88831)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 19.1.7 (3+b2)     Debian flang-new version 19.1.7 (3+b2)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘MiscMetabar/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘MiscMetabar’ version ‘0.14.3’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [3s/4s] OK
• 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 ... OK See the install log for details.
• 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 code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [17s/22s] OK
• checking whether the package can be loaded with stated dependencies ... [17s/22s] OK
• checking whether the package can be unloaded cleanly ... [16s/21s] OK
• checking whether the namespace can be loaded with stated dependencies ... [17s/22s] OK
• checking whether the namespace can be unloaded cleanly ... [18s/23s] OK
• checking loading without being on the library search path ... [18s/27s] 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 ... [93s/111s] OK
• checking Rd files ... [2s/2s] 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 ... [9s/11s] 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 ... [150s/184s] OK Examples with CPU (user + system) or elapsed time > 5s                           user system elapsed SRS_curve_pq 8.993 0.358 11.117 ggscatt_pq 7.151 0.030 8.878 tbl_sum_taxtable 6.800 0.012 8.671 psmelt_samples_pq 6.061 0.123 6.734 plot_refseq_extremity_pq 6.120 0.028 7.644 LCBD_pq 5.443 0.255 7.608 plot_complexity_pq 5.591 0.032 6.890 subset_taxa_tax_control 5.490 0.126 7.163 tbl_sum_samdata 4.918 0.028 6.560 sankey_pq 4.412 0.066 5.978 hill_curves_pq 4.387 0.003 5.998
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [119s/81s] ERROR   Running ‘spelling.R’ [0s/0s]   Running ‘testthat.R’ [119s/80s] 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      Loading required package: purrr      Attaching package: 'purrr'      The following object is masked from 'package:testthat':          is_null      >   > test_check("MiscMetabar")   Starting 2 test processes   [ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]      ══ Skipped tests (74) ══════════════════════════════════════════════════════════   • On CRAN (74): 'test_adonis.R:1:1', 'test_controls.R:7:3',     'test_controls.R:14:3', 'test_controls.R:46:3', 'test_deprecated.R:1:1',     'test_clean_pq.R:8:3', 'test_clean_pq.R:17:3',     'test_figures_alpha_div.R:17:3', 'test_figures_alpha_div.R:63:3',     'test_figures_alpha_div.R:73:3', 'test_figures_alpha_div.R:95:3',     'test_figures_alpha_div.R:122:3', 'test_figures_alpha_div.R:151:3',     'test_figures_alpha_div.R:157:3', 'test_deseq2_edgeR.R:16:5',     'test_deseq2_edgeR.R:25:3', 'test_deseq2_edgeR.R:48:5',     'test_deseq2_edgeR.R:59:3', 'test_figures_biplot.R:14:3',     'test_figures_biplot.R:52:3', 'test_figures_misc.R:11:3',     'test_figures_misc.R:19:3', 'test_figures_misc.R:26:3',     'test_figures_misc.R:35:3', 'test_figures_summary_plot.R:9:3',     'test_figures_summary_plot.R:19:3', 'test_figures_summary_plot.R:28:3',     'test_figures_beta_div.R:22:3', 'test_figures_beta_div.R:73:5',     'test_figures_beta_div.R:92:3', 'test_figures_beta_div.R:102:5',     'test_figures_beta_div.R:159:5', 'test_figures_beta_div.R:209:3',     'test_figures_beta_div.R:241:5', 'test_figures_beta_div.R:259:5',     'test_figures_beta_div.R:289:5', 'test_figures_beta_div.R:314:3',     'test_figures_beta_div.R:346:3', 'test_figures_beta_div.R:355:3',     'test_figures_beta_div.R:387:3', 'test_figures_beta_div.R:402:3',     'test_figures_beta_div.R:414:3', 'test_krona.R:7:3',     'test_figures_taxo.R:64:3', 'test_figures_taxo.R:165:3',     'test_figures_taxo.R:209:5', 'test_figures_taxo.R:252:5',     'test_figures_taxo.R:319:5', 'test_figures_taxo.R:354:3',     'test_figures_taxo.R:379:3', 'test_figures_taxo.R:414:3',     'test_phyloseq_class.R:10:3', 'test_phyloseq_class.R:51:3',     'test_phyloseq_class.R:95:3', 'test_rw.R:8:3', 'test_rw.R:24:3',     'test_rw.R:39:3', 'test_subset.R:7:3', 'test_subset.R:18:3',     'test_table_functions.R:6:3', 'test_table_functions.R:19:3',     'test_table_functions.R:34:5', 'test_table_functions.R:47:5',     'test_targets.R:5:3', 'test_targets.R:56:3', 'test_targets.R:84:3',     'test_targets.R:101:3', 'test_targets.R:111:3', 'test_tuckey.R:5:3',     'test_tuckey.R:17:3', 'test_tuckey.R:26:3', 'test_misc.R:11:3',     'test_misc.R:30:3', 'test_misc.R:97:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Failure ('test_figures_beta_div.R:72:5'): graph_test_pq works ───────────────   `graph_test_pq(data_fungi_mini, fact = "Tree_name")` produced warnings.      [ FAIL 1 | WARN 2 | SKIP 74 | PASS 82 ]   Error: Test failures   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [29s/35s] OK
• checking PDF version of manual ... [16s/21s] OK
• checking HTML version of manual ... [7s/12s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR