MelonnPan installation on ubuntu 20.04 issues

Microbial community profiling MelonnPan
1

Hello,
I tried to install MelonnPan on ubuntu 20.04 subsystem for Windows following the instructions presented in the tutorial (melonnpan · biobakery/biobakery Wiki · GitHub), trying with both R versions 4.1.2 and 3.6.1 in two different conda environments.
I had problems as I attempted to install the packages listed:

R -q -e "install.packages(c('devtools', 'glmnet', 'foreach', 'getopt', 'doParallel', 'vegan', 'data.table', 'ggplot2', 'AssocTests', 'optparse', 'tibble'), repos='http://cran.r-project.org')"

And in the end I got this error for some of the packages:

ERROR: dependency ‘credentials’ is not available for package ‘gert’

  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/gert’
    ERROR: dependency ‘httr’ is not available for package ‘gh’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/gh’
    ERROR: dependencies ‘systemfonts’, ‘textshaping’ are not available for package ‘ragg’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/ragg’
    ERROR: dependency ‘fExtremes’ is not available for package ‘AssocTests’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/AssocTests’
    ERROR: dependencies ‘curl’, ‘gert’, ‘gh’ are not available for package ‘usethis’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/usethis’
    ERROR: dependencies ‘httr’, ‘ragg’ are not available for package ‘pkgdown’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/pkgdown’
    ERROR: dependencies ‘usethis’, ‘pkgdown’, ‘rcmdcheck’, ‘rversions’, ‘urlchecker’ are not available for package ‘devtools’
  • removing ‘/home/studenti/miniconda3/envs/biobakery-melonnpan/lib/R/library/devtools’

The downloaded source packages are in
‘/tmp/Rtmp1XU3Vb/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making ‘packages.html’ … done
There were 19 warnings (use warnings() to see them)

I tried manually installing them in R using install.packages(“package”, dependencies=TRUE), but I got the same output.
How can I make the dependencies available for the packages I need to run MelonnPan?

Thank you

2

Hi @AndreaGatti - you need to install each and every package manually until all the dependencies are installed. In particular, anytime you see that dependency XXXX is not available for package ‘YYYY’, you need to manually install XXXX before installing YYYY. Hope this helps!

3

Thank you, I tried to manually install all the dependencies packages, but got no better result.
Nonetheless, I understood that the problem regarded installation paths, so, with a few attempts, I could install everything.
Thank you anyway for the quick support!