installation error in R 3.6.3

[shakti83kumar]

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 in 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

[jbisanz]

Hmm. A couple simultaneous issues. As a quick work around, you can install these packages manually from bioconductor and/or manually reinstalling survival manually. I will look into this in more detail in the future.