MicrobeR v0.3-Installation

install

(Fabiola ) #1

Hello,

I have a quick question, I am trying to install MicrobeR, but it is not working. I followed the instruction in the tutorials, but I get the error below.

library(devtools)
install_github(“jbisanz/MicrobeR”)
Downloading GitHub repo jbisanz/[email protected]
from URL https://api.github.com/repos/jbisanz/MicrobeR/zipball/master
Installing MicrobeR
“C:/Users/fabipc/DOCUME~1/R/R-35~1.1/bin/x64/R” --no-site-file
–no-environ --no-save --no-restore --quiet CMD INSTALL
“C:/Users/fabipc/AppData/Local/Temp/RtmpkDzy4y/devtools26f4c72134/jbisanz-MicrobeR-5d5cd5d”
–library=“C:/Users/fabipc/Documents/R/R-3.5.1/library”
–install-tests

ERROR: dependencies ‘philr’, ‘DECIPHER’ are not available for package ‘MicrobeR’

  • removing ‘C:/Users/fabipc/Documents/R/R-3.5.1/library/MicrobeR’
    In R CMD INSTALL
    Installation failed: Command failed (1)

Thanks


(benjamin w.) #2

try running

install.packages(philr)
install.packages(DECIPHER)

and re-running

library(philr)
library(DECIPHER)


(Fabiola ) #3

Hi Ben,

Thanks for the quick response. When I try to install them, it get this error
Error in install.packages : object ‘DECIPHER’ not found

install.packages(“philr”)
Warning in install.packages :
package ‘philr’ is not available (for R version 3.5.1)
install(DECIPHER)


(benjamin w.) #4

Oh, philr is bioClite

source(“https://bioconductor.org/biocLite.R”)
biocLite(“philr”)

try installing philr that way

source(“https://bioconductor.org/biocLite.R”)
biocLite(“DECIPHER”)



(Fabiola ) #5

Sorry for the dumb question, but I have never installed a package like this. I tried install.packages (biocLite(“DECIPHER”)) and just biocLite(“DECIPHER”) and it didn’t work.


(benjamin w.) #6

No problem,

You have to tell R to open the source:

Run this first:

source(“https://bioconductor.org/biocLite.R”)

Once R opens the source, you can just run:

biocLite(“philr”)
biocLite(“DECIPHER”)

Please let me know if this works! Ben


(Jordan Bisanz) #7
source("https://bioconductor.org/biocLite.R")
biocLite("DECIPHER")

This should install DECIPHER. MicrobeR is a swiss-army knife of sorts to streamline certain tasks or to help visualize and as such it has quite a long list of dependencies. Running the code below might help fill in any missing dependencies. Note, if you are using an unix operating system it will also download some extra sequencing data.

source("https://raw.githubusercontent.com/jbisanz/BMS270_2018/master/InstallTutorial.R")

(Fabiola ) #8

Yeih! That worked :slight_smile:
Thank you very much for all your help