Loading microbiome data into R

source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.6 (BiocInstaller 1.28.0),
  ?biocLite for help
A new version of Bioconductor is available after
  installing the most recent version of R; see
  http://bioconductor.org/install

biocLite("biomformat")

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.4
  (2018-03-15).
Installing package(s) <U+393C><U+3E31>biomformat<U+393C><U+3E32>
package <U+393C><U+3E31>biomformat<U+393C><U+3E32> is in use and will not be installedinstallation path not writeable, unable to update
  packages: cluster, foreign, MASS, Matrix, nlme,
  survival
Old packages: 'data.table', 'stringi'

Update all/some/none? [a/s/n]: 

setwd("C:/Users/tropa/Desktop/otu_open_ref")

Update all/some/none? [a/s/n]: 

a

  There are binary versions available but the
  source versions are later:
           binary source needs_compilation
data.table 1.11.0 1.11.2              TRUE
stringi     1.1.7  1.2.2              TRUE

  Binaries will be installed

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/data.table_1.11.0.zip'
Content type 'application/zip' length 1809969 bytes (1.7 MB)
downloaded 1.7 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.4/stringi_1.1.7.zip'
Content type 'application/zip' length 14295248 bytes (13.6 MB)
downloaded 13.6 MB

package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘stringi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\tropa\AppData\Local\Temp\RtmpczR1ws\downloaded_packages

library('biomformat')

biom convert -i otu_table_mc2_w_tax.biom -o otu_table_json.biom --to-json

silva.otus.biom <- read_biom('../otu_table_json.biom')

Error in read_biom("../otu_table_json.biom") :
  Both attempts to read input file:
../otu_table_json.biom
either as JSON (BIOM-v1) or HDF5 (BIOM-v2).
Check file path, file name, file itself, then try again.