Error

biom convert ...

bash: biom: command not found...

Error while running CSS normalisation

normalize_table.py -i otu_table.biom -a CSS -o otu_table_CSSnorm.biom

Library biom not found.

To install, open R and run the command:

install.packages("biom")

If you already have the biom package installed in a local directory,

please store the path to that directory in an environment variable

called "R_LIBRARY_PATH". This may be necessary if you are running

QIIME on a cluster, and the cluster instances of R don't know about

your local R libraries. If you don't know your R library paths, you

can list them by opening R and running with the command, ".libPaths()".

The current R instance knows about these paths:

[/usr/lib64/R/library, /usr/share/R/library]

Warning message:

In library(lib.name, character.only = TRUE, logical.return = TRUE, :

there is no package called ‘biom’

Problem: biom package is not installed in R

"Package ‘biom’ was removed from the CRAN repository."

https://cran.r-project.org/web/packages/biom/index.html

Solution

Update 2020

install R package biomformat

if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("biomformat")

https://www.bioconductor.org/packages/release/bioc/html/biomformat.html

Solution of 2019

install development version of the R biom package

1) install libssl libcurl libxml on linux

sudo apt-get install libssl-dev curl libcurl4-openssl-dev libxml2-dev # Debian/Ubuntu

sudo yum install -y openssl-devel curl libcurl libcurl-devel libxml2 libxml2-devel # CentOS

2) In R: install development tools

to be able to download and install biom from git

R

install.packages("devtools")

library("devtools")

install_github("joey711/biom")

https://www.r-project.org/nosvn/pandoc/biom.html

# Error in R

Warning messages:

1: In install.packages("devtools") :

installation of package ‘curl’ had non-zero exit status

2: In install.packages("devtools") :

installation of package ‘openssl’ had non-zero exit status

3: In install.packages("devtools") :

installation of package ‘git2r’ had non-zero exit status

4: In install.packages("devtools") :

installation of package ‘httr’ had non-zero exit status

5: In install.packages("devtools") :

installation of package ‘devtools’ had non-zero exit status

# requires Linux/Ubuntu installation of libssl libcurl and libxml, see (1) above.