Problem to load

[Sirbius]

Hi there,

I installed microbiomeutilities on our Rocky Linux 9 system, with R version 4.3.2.
I did not get any ERROR but only warinigs:

`> devtools::install_github("microsud/microbiomeutilities",force=T)
Downloading GitHub repo microsud/microbiomeutilities@HEAD
Skipping 3 packages not available: Biostrings, microbiome, phyloseq
── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/Rtmp89BVzJ/remotes63a264c7e39b/microsud-microbiomeutilities-046a9f9/DESCRIPTION’ ...
─ preparing ‘microbiomeutilities’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘microbiomeutilities_1.00.17.tar.gz’

Installing package into ‘/home/silviat/R/x86_64-redhat-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)

• installing source package ‘microbiomeutilities’ ...
  ** using staged installation
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** byte-compile and prepare package for lazy loading
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘microbiome::alpha’ when loading ‘microbiomeutilities’
  ** help
  *** installing help indices
  converting help for package ‘microbiomeutilities’
  finding HTML links ... done
  add_refseq html
  finding level-2 HTML links ... done

  aggregate_top_taxa2 html
  dominant_taxa html
  find_samples_taxa html
  format_to_besthit html
  get_group_abundances html
  get_microbiome_data html
  get_tibble html
  hmp2 html
  join_otu_tax html
  list_microbiome_data html
  make_pairs html
  peak-methods html
  percent_classified html
  phy_to_ldf html
  plasticity html
  plot_abund_prev html
  plot_alpha_diversities html
  plot_alpha_rcurve html
  plot_area html
  plot_diversity_stats html
  plot_listed_taxa html
  plot_ordination_utils html
  plot_ordiplot_core html
  plot_paired_abundances html
  plot_read_distribution html
  plot_select_taxa html
  plot_spaghetti html
  plot_taxa_boxplot html
  plot_taxa_composition html
  plot_taxa_cv html
  plot_taxa_heatmap html
  prep_tern_otu html
  prep_ternary html
  print_ps html
  rarefy_util html
  simple_heatmap html
  taxa_distribution html
  taxa_pooler_mcola html
  taxa_summary html
  theme_biome_utils html
  zackular2014 html
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘microbiome::alpha’ when loading ‘microbiomeutilities’
  ** testing if installed package can be loaded from final location
  Warning: replacing previous import ‘ggplot2::alpha’ by ‘microbiome::alpha’ when loading ‘microbiomeutilities’
  ** testing if installed package keeps a record of temporary installation path

• DONE (microbiomeutilities)`

But if I then load the package:
library("microbiomeutilities")
I get:

library("microbiomeutilities")
Error: package or namespace load failed for ‘microbiomeutilities’:
(converted from warning) replacing previous import ‘ggplot2::alpha’ by ‘microbiome::alpha’ when loading ‘microbiomeutilities’

What could be the problem??
Thanks

[gutmicrobe]

Thanks for using out tool. The error is likely caused by not having Bioconductor repos accessible for Biostrings, microbiome, phyloseq in your linux environment.
Try the following order of installation.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phyloseq")
BiocManager::install("microbiome")

and then install mirobiomeutilties from github.
Alternatively, I would like to direct your attention to the new microbiome data science framework (recommended) that is actively maintained here https://microbiome.github.io/OMA/