Isse in importing Qiime2 and Biom dada with "could not find function 'read_biom' " error.

[jrhaulung]

Dear Dr. Chen,

I'm writing to you because I'm encountering an issue with MicrobiomeStat and hope you can offer some guidance.

I've successfully installed MicrobiomeStat (version 1.4.1) in a Conda environment, following the instructions to install the necessary 27 R packages and then using devtools::install_github("cafferychen777/MicrobiomeStat"). The installation completed without errors.

However, when I attempt to import data using either the QIIME2 or BIOM file import procedures outlined in the MicrobiomeStat tutorials (links 1 and 2 below), I consistently receive a "could not find function 'read_biom'" error.

QIIME2 import error:

Unzipping the .qza file...
Locating the metadata file...
Reading the metadata...
Processing the file based on its format...
Error in read_biom(file) : could not find function "read_biom"

BIOM import error:

Error in read_biom(biom_file = BIOMfilename) :
  could not find function "read_biom"

I also tried installing the phyloseq package, as suggested in GitHub Issue #34, but the error persists.

I apologize for bothering you with this, especially since it's an initial setup hurdle. Any help you could provide would be greatly appreciated.

Thank you,

Jrhau

Tutorial Links:

https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/importing-data-from-qiime2-into-microbiomestat

https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/transferring-data-from-biom-into-microbiomestat

[jrhaulung]

Loading Biostrings, yaml, and biomformat using library(Biostrings), library(yaml), and library(biomformat) respectively appears to resolve the issue.

[cafferychen777]

Hi @jrhaulung,

Thank you for reporting this issue and for finding the solution! You're absolutely correct - the read_biom function requires the biomformat package to be loaded.

As you discovered, loading the required packages:

library(Biostrings)
library(yaml)
library(biomformat)

resolves the issue. These dependencies are actually documented in our installation guide at:
https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/kick-start-your-journey-the-microbiomestat-installation-guide

The installation guide includes all 27 required R packages that need to be installed for MicrobiomeStat to function properly. I recommend following the complete installation procedure outlined there to ensure all dependencies are properly set up.

Thank you for sharing your solution - it will definitely help other users who encounter the same issue!

Best regards,
Chen