Error(s) in re-building vignettes:
  ...
--- re-building ‘functional_prediction.Rmd’ using rmarkdown
Quitting from lines 37-39 (functional_prediction.Rmd) 
Error: processing vignette ‘functional_prediction.Rmd’ failed with diagnostics:
download from ‘https://gitlab.com/sw1/themetagenomics_data/raw/master/ko_13_5_precalculated.tab.gz’ failed
--- failed re-building ‘functional_prediction.Rmd’

--- re-building ‘thematic_structure.Rmd’ using rmarkdown
--- finished re-building ‘thematic_structure.Rmd’

SUMMARY: processing the following file failed:
  ‘functional_prediction.Rmd’

Error: Vignette re-building failed.
Execution halted
Undeclared package ‘glmnet’ in Rd xrefs
Package required but not available: 'lme4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc          1.0Mb
    libs         2.2Mb
    references   1.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc          1.0Mb
    libs         2.2Mb
    references   1.1Mb