I got this:
/home/mothur/.Rprofile
which is weird because we also tried to delete R, and apparently is still there... The previous person working on the server installed R and dada2... this why "/home/mothur". However my knowledge about virtual machines is scarce... but I'm suspecting some interactions of R dependencies.
I also tried yesterday with Atacama tutorial, in case the problem were because of the sample nature, but same error as usual, in DADA2 with R. Anyway there is something good, I tried today Atacama with Deblur following Analyzing paired end reads in QIIME 2 and it worked (got table, sequences data and stats.qza!). So there is something working 
Thanks @thermokarst
Ps. QIIME2 have been also upgraded to qiime2-2017.11