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I've installed a program from a .tar.gz package (biom, because even though it's outdated I need it for a qiime script). Problem is that when I run the qiime script, R is looking in different sources

(/home/username/R/x86_64-pc-linux-gnu-library/3.4, /home/username/anaconda2/lib/R/library)

than the R instance that I've installed (3.30), which is looking in

("/home/username/R/x86_64-pc-linux-gnu-library/3.3" "/usr/local/lib/R/site-library" "/usr/lib/R/site-library" "/usr/lib/R/library")

Biom is installed in /home/username/R/x86_64-pc-linux-gnu-library/3.3, so the qiime R-instance can't see it. How can I get qiime's R to see biom?

I've tried downgrading my R instance from 3.5, which does not support biom, to 3.3, which does.

Austin McDonald
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  • Is “biom” an R package or an external program? Because the paths you show are *package library* paths. If it’s a package, the solution is to install it using the QIIME R (presumably installed using Conda), rather than your other R installation. This might imply installing an older version of R via Conda but your question doesn’t make clear whether that was successful. – Konrad Rudolph Mar 29 '19 at 15:38
  • biom is an R package – Austin McDonald Mar 29 '19 at 15:40

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