cmultRepl from zCompositions error in the expected output argument "counts"

Error in match.arg(output) : 'arg' should be one of “prop”, “p-counts”

Dec 02 '19 18:12 jmmack

Appears "counts" is no longer valid option in newer zCompositions version, can you confirm that "p-counts" is equivalent?

Dec 02 '19 18:12 jbisanz

I'm using zCompositions 1.3.3 and p-counts works

Dec 02 '19 19:12 jmmack

Hi jbisanz , I want to run MicrobeR. I tried to install by following command as mentioned in file:///home/adapt/MicrobeR/index.html. I am installing it R 3.6.3 version. library(devtools) install_github("jbisanz/MicrobeR") I got following ERROR: devtools::install_github("jbisanz/MicrobeR") Downloading GitHub repo jbisanz/MicrobeR@master Skipping 4 packages not available: philr, DECIPHER, phyloseq, Biostrings Installing 2 packages: zCompositions, NADA Installing packages into ‘/home/adapt/R/x86_64-pc-linux-gnu-library/3.6’ (as ‘lib’ is unspecified) trying URL 'https://cloud.r-project.org/src/contrib/zCompositions_1.3.4.tar.gz' Content type 'application/x-gzip' length 49330 bytes (48 KB)

downloaded 48 KB

trying URL 'https://cloud.r-project.org/src/contrib/NADA_1.6-1.tar.gz' Content type 'application/x-gzip' length 71559 bytes (69 KB)

downloaded 69 KB

installing source package ‘NADA’ ... ** package ‘NADA’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** data ** byte-compile and prepare package for lazy loading Error: package or namespace load failed for ‘survival’: package ‘survival’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version Error: package ‘survival’ could not be loaded Execution halted ERROR: lazy loading failed for package ‘NADA’
removing ‘/home/adapt/R/x86_64-pc-linux-gnu-library/3.6/NADA’ Error: Failed to install 'MicrobeR' from GitHub: (converted from warning) installation of package ‘NADA’ had non-zero exit status

Mar 20 '20 04:03 shakti83kumar