* using log directory ‘/srv/hornik/tmp/CRAN_pretest/MiscMetabar.Rcheck’
* using R Under development (unstable) (2024-09-03 r87093)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 18.1.8 (9)
    Debian flang-new version 18.1.8 (9)
* 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 ‘0.9.3’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [7s/12s] NOTE
Maintainer: ‘Adrien Taudière <adrien.taudiere@zaclys.net>’

Found the following (possibly) invalid URLs:
  URL: https://www.sciencedirect.com/science/article/abs/pii/S1754504815000847
    From: man/add_funguild_info.Rd
          man/get_funguild_db.Rd
    Status: 403
    Message: Forbidden
* 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 code 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 ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] 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 ... [36s/36s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  LCBD_pq.Rd: phyloseq-class
  SRS_curve_pq.Rd: phyloseq-class
  accu_plot.Rd: phyloseq-class, ggplot
  accu_plot_balanced_modality.Rd: phyloseq-class
  add_blast_info.Rd: phyloseq-class
  add_dna_to_phyloseq.Rd: phyloseq-class
  add_funguild_info.Rd: phyloseq-class
  add_info_to_sam_data.Rd: phyloseq-class
  add_new_taxonomy_pq.Rd: phyloseq-class
  adonis_pq.Rd: phyloseq-class
  adonis_rarperm_pq.Rd: phyloseq-class
  ancombc_pq.Rd: phyloseq-class
  are_modality_even_depth.Rd: phyloseq-class
  as_binary_otu_table.Rd: phyloseq-class
  biplot_pq.Rd: phyloseq-class
  blast_pq.Rd: phyloseq-class
  blast_to_derep.Rd: derep-class
  blast_to_phyloseq.Rd: phyloseq-class
  build_phytree_pq.Rd: phyloseq-class
  circle_pq.Rd: phyloseq-class
  clean_pq.Rd: phyloseq-class
  compare_pairs_pq.Rd: phyloseq-class
  dist_pos_control.Rd: phyloseq-class
  distri_1_taxa.Rd: phyloseq-class
  filter_asv_blast.Rd: phyloseq-class
  formattable_pq.Rd: phyloseq-class
  ggaluv_pq.Rd: phyloseq-class
  ggbetween_pq.Rd: phyloseq-class
  ggscatt_pq.Rd: phyloseq-class
  ggvenn_pq.Rd: phyloseq-class, ggplot
  glmutli_pq.Rd: phyloseq-class
  graph_test_pq.Rd: phyloseq-class, ggplot
  heat_tree_pq.Rd: phyloseq-class
  hill_pq.Rd: phyloseq-class
  hill_test_rarperm_pq.Rd: phyloseq-class
  hill_tuckey_pq.Rd: phyloseq-class
  iNEXT_pq.Rd: phyloseq-class
  krona.Rd: phyloseq-class
  lulu_pq.Rd: phyloseq-class
  multi_biplot_pq.Rd: phyloseq-class
  multipatt_pq.Rd: phyloseq-class
  multitax_bar_pq.Rd: phyloseq-class
  mumu_pq.Rd: phyloseq-class
  normalize_prop_pq.Rd: phyloseq-class
  phyloseq_to_edgeR.Rd: phyloseq-class
  physeq_or_string_to_dna.Rd: phyloseq-class
  plot_LCBD_pq.Rd: phyloseq-class
  plot_SCBD_pq.Rd: phyloseq-class
  plot_ancombc_pq.Rd: phyloseq-class
  plot_deseq2_pq.Rd: phyloseq-class, ggplot
  plot_edgeR_pq.Rd: phyloseq-class, ggplot
  plot_guild_pq.Rd: phyloseq-class
  plot_mt.Rd: ggplot
  plot_tax_pq.Rd: phyloseq-class
  plot_tsne_pq.Rd: phyloseq-class
  postcluster_pq.Rd: phyloseq-class
  psmelt_samples_pq.Rd: phyloseq-class
  rarefy_sample_count_by_modality.Rd: phyloseq-class
  rename_samples_otu_table.Rd: phyloseq-class
  reorder_taxa_pq.Rd: phyloseq-class
  ridges_pq.Rd: phyloseq-class, ggplot
  rotl_pq.Rd: phyloseq-class
  sankey_pq.Rd: phyloseq-class
  save_pq.Rd: phyloseq-class
  search_exact_seq_pq.Rd: phyloseq-class
  select_one_sample.Rd: phyloseq-class
  simplify_taxo.Rd: phyloseq-class
  subset_samples_pq.Rd: phyloseq-class
  subset_taxa_pq.Rd: phyloseq-class
  subset_taxa_tax_control.Rd: phyloseq-class
  summary_plot_pq.Rd: phyloseq-class
  swarm_clustering.Rd: phyloseq-class
  tax_bar_pq.Rd: phyloseq-class, ggplot
  tax_datatable.Rd: phyloseq-class
  taxa_as_columns.Rd: phyloseq-class
  taxa_as_rows.Rd: phyloseq-class
  taxa_only_in_one_level.Rd: phyloseq-class
  tbl_sum_samdata.Rd: phyloseq-class
  treemap_pq.Rd: phyloseq-class
  tsne_pq.Rd: phyloseq-class
  upset_pq.Rd: phyloseq-class, ggplot
  upset_test_pq.Rd: phyloseq-class, ggplot
  var_par_pq.Rd: phyloseq-class
  var_par_rarperm_pq.Rd: phyloseq-class
  venn_pq.Rd: phyloseq-class, ggplot
  verify_pq.Rd: phyloseq-class
  vs_search_global.Rd: phyloseq-class
  vsearch_clustering.Rd: phyloseq-class
  write_pq.Rd: phyloseq-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... [116s/116s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [52s/29s] OK
  Running ‘testthat.R’ [52s/29s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [11s/11s] 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: 2 NOTEs