MicrobeR v0.3-Installation

Other Bioinformatics Tools
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/MicrobeR@master
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

1 Like
2

try running

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

and re-running

library(philr)
library(DECIPHER)

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)

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")

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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.

1 Like
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

1 Like
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")
2 Likes
8

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

2 Likes
9

I was able to instamm MicrobeR but the tutorial is based on a preinstalled data in R so it is a bit confusing to figure out how to import our own files (especially QIIME2 format) and what file to import. Can you explain that?

10

Hello @jbisanz,

I've been using your tutorial qiime2R and it worked really great with my data, thank you so much... :slight_smile:

I'm using Version 1.2.1335 of RStudio, on MacOS Mojave Version 10.14.5 (18F132).

But I'm having trouble with installing MicrobeR. I've installed required philr and Decipher, that was fine, but I still get this error when I get to installation of MicrobeR (it starts fine then I get the error):

"* installing source package ‘MicrobeR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Error: .onLoad failed in loadNamespace() for 'rjags', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.so, 10): Library not loaded: /usr/local/lib/libjags.4.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/3.6/Resources/library/rjags/libs/rjags.so
Reason: image not found
Execution halted
ERROR: lazy loading failed for package ‘MicrobeR’

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/MicrobeR’
    Error in i.p(...) :
    (converted from warning) installation of package ‘/var/folders/pn/zcr4hs9x7c761blcsx_z0jfr0000gn/T//Rtmp9kr9yR/file93aa1f80bc50/MicrobeR_0.3.2.tar.gz’ had non-zero exit status"

I suspect that this error is connected to my being unable to install tibble package, which gives me this error:
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
ERROR: compilation failed for package ‘tibble’

  • removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/tibble’
    Error in i.p(...) :
    (converted from warning) installation of package ‘tibble’ had non-zero exit status

But I'm not sure... I had it installed, then I removed it, it gives the same error over and over again. As you can see, I'm not R savvy, but I can follow instructions.

Thanks for any help!

11

I think it might be related to missing some part of xcode. You can download the full version from the app store, or if space is an issue, I think you can download just the command line tools via the bash terminal with xcode-select --install.

12

Hi, hope you had a nice weekend.

I dowloaded the Xcode and run the xcode-select --install command and installed command line tools in Terminal.
Still have the same issue:

"Error in i.p(...) :
(converted from warning) installation of package ‘/var/folders/pn/zcr4hs9x7c761blcsx_z0jfr0000gn/T//Rtmp01CNOr/file9d9b396d3d7e/MicrobeR_0.3.2.tar.gz’ had non-zero exit status"

Thanks for the help.

Btw, I tried numerous other things, like just now I dowloaded zip file and tried to installed it locally but it gave me the same error.

Also, during install it gives me this: Skipping 4 packages not available: Biostrings, DECIPHER, philr, phyloseq.
I dowloaded all the mentioned packeges multiple times and called them with library, so I don't get it...

13

Hi, I resolved the issue finally, I'll post the solution in case other users encounter it:

  1. Dowloading and installation of this package: JAGS: Just Another Gibbs Sampler - Browse /JAGS/4.x/Mac OS X at SourceForge.net

  2. Running this in Rstudio:

devtools::install_url("Download rjags_4-4.tar.gz (JAGS: Just Another Gibbs Sampler)",
args="--configure-args='--with-jags-include=/Users/casallas/homebrew/opt/jags/include/JAGS
--with-jags-lib=/Users/casallas/homebrew/opt/jags/lib'
"
)

library(rjags)
library(Biostrings)
library(DECIPHER)
library(philr)
library(phyloseq)
library(devtools)

install_github("jbisanz/MicrobeR", type = "binary")

library(MicrobeR)

3 Likes
14

Weird! Thanks for trouble shooting this and I will try to look into why it happened at a later date.

Thanks,

Jordan

1 Like