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biocore / biom-format

The Biological Observation Matrix (BIOM) Format Project
http://biom-format.org
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error in importing biom file from QIIME to R using the biom package #711

Closed mingjiew closed 8 years ago

mingjiew commented 8 years ago

I am trying to use the 'biom' package to import a biom file generated by QIIME to R (3.2.3).

biom_file <- system.file("extdata", "out.biom", package = "biom")

x = read_biom(biom_file)

Error in fromJSON(content, handler, default.size, depth, allowComments, :

invalid JSON input

Do you know the reason for the error? I even used biom convert in QIIME to explicitly convert the biom file into JSON format and still it has the same error. I know the 'biomformat' package might be better, but for now I need to use R 3.2.3.

wasade commented 8 years ago

Closing as off topic, this repository does not maintain the R biom library. From looking at their github repo, however, it appears a parallel issue was already created there