Qiime - problem with biom package in normalization

Question

[kperlejewski]

Hi,

I want to use Qiime DESeq2 normalization by command. I need to install "biom" package in R to make it work iut I have this comment:

Warning message: package ‘biom’ is not available (for R version 3.5.0)

What can I do with that? It's the newest R version.

Answer 1

[Dattatray Mongad]

biom package is not supported now. You can download it from here and install it manually using install.packages() cmd in R.

[Payal]

How to do that ?

I typed:

install.packages(biom_0.3.8.tar.gz) Error in install.packages(biom_0.3.8.tar.gz) : object 'biom_0.3.8.tar.gz' not found

Answer 2

[zx8754]

Relevant post, with many many reasons:

• StackOverflow: How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning?

And CRAN says it is archived, so the question is:

• StackOverflow: How do I install a package that has been archived from CRAN?

Answer 3

[Leonardo]

I've just got into this issue while installing Tax4Fun and that's how I fixed (R 3.5.3):

Went to the development page on GitHub: https://github.com/joey711/biom Then "made available through Cran" and there "archive". Downloaded the latest version (biom 0.3.12.tar.gz)

Installing:

install.packages("path_to_the_file/biom_0.3.12.tar.gz", repos = NULL, type = "source", dependencies = T) 
#in RStudio Tools->InstallPackages->InstallFromPackageArchive

It still complained about not having the dependency RJSONIO available. Then:

install.packages("RJSONIO")

Then again install.packages("path_to_the_file/biom_0.3.12.tar.gz", repos = NULL, type = "source", dependencies = T) and it worked.

Cheers for future users =)