Question: Qiime - problem with biom package in normalization
0
gravatar for kperlejewski
23 months ago by
kperlejewski0 wrote:

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.

qiime biom R • 1.4k views
ADD COMMENTlink modified 11 months ago by Leonardo30 • written 23 months ago by kperlejewski0
1
gravatar for Dattatray Mongad
23 months ago by
National Centre for Cell Science, Pune
Dattatray Mongad350 wrote:

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

ADD COMMENTlink written 23 months ago by Dattatray Mongad350

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

ADD REPLYlink written 19 months ago by Payal80
0
gravatar for zx8754
23 months ago by
zx87549.4k
London
zx87549.4k wrote:

Relevant post, with many many reasons:

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

ADD COMMENTlink modified 23 months ago • written 23 months ago by zx87549.4k
0
gravatar for Leonardo
11 months ago by
Leonardo30
Brazil
Leonardo30 wrote:

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 =)

ADD COMMENTlink written 11 months ago by Leonardo30
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