Cannot install qiime2R on R version 3.6.1

Hi all!

I have a problem with qiime2R installation in R studio with R version 3.6.1.

Here is the code I’ve used:

install.packages(“devtools”)
devtools::install_github(“jbisanz/qiime2R”)

Devtools were installed correctly but I have a problem with second command which which gives me this error:

Error: (converted from warning) Setting LC_CTYPE failed, using “C”
Execution halted
Error: Failed to install ‘qiime2R’ from GitHub:
(converted from warning) installation of package ‘/var/folders/7y/3bk0drr50qq6dmdb4hr3gwv40000gn/T//RtmpI7EjxB/file198a4cfab921/qiime2R_0.99.12.tar.gz’ had non-zero exit status

Any idea, how I can solve this problem?

Best,
Agata

Hi Agata,

This appears to be an issue with R perhaps relating to settings for language. Which operating system are you using? This might help: https://stackoverflow.com/questions/9689104/installing-r-on-mac-warning-messages-setting-lc-ctype-failed-using-c.

Jordan

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Yes, that helped!

Thank you, Best, Agata

Hi Jbisanz,

I met the same problem.

` download.file(“https://github.com/jbisanz/qiime2R/archive/master.zip”, “source.zip”)
trying URL ‘https://github.com/jbisanz/qiime2R/archive/master.zip
Content type ‘application/zip’ length 2751675 bytes (2.6 MB)
downloaded 2.6 MB

unzip(“source.zip”)
install.packages(“qiime2R-master”, repos = NULL, type=“source”,dependencies = TRUE)
Installing package into ‘\freja/homedir$/yundum/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

  • installing source package ‘qiime2R’ …
    ** using staged installation
    Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone ‘GMT’
    ** R
    ** inst
    Warning in file.create(to[okay]) :
    cannot create file ‘\freja/homedir$/yundum/Documents/R/win-library/3.6/00LOCK-qiime2R-master/00new/qiime2R/CITATION’, reason ‘No such file or directory’
    Warning in file.create(to[okay]) :
    cannot create file ‘\freja/homedir$/yundum/Documents/R/win-library/3.6/00LOCK-qiime2R-master/00new/qiime2R/NEWS’, reason ‘No such file or directory’
    ** byte-compile and prepare package for lazy loading
    Error in findpack(package, lib.loc) :
    there is no package called ‘qiime2R’
    Calls: -> findpack
    Execution halted
    ERROR: lazy loading failed for package ‘qiime2R’
  • removing ‘\freja/homedir$/yundum/Documents/R/win-library/3.6/qiime2R’
    Warning in install.packages :
    installation of package ‘qiime2R-master’ had non-zero exit statusThe R version info is as below> version
    _
    platform x86_64-w64-mingw32
    arch x86_64
    os mingw32
    system x86_64, mingw32
    status
    major 3
    minor 6.1
    year 2019
    month 07
    day 05
    svn rev 76782
    language R
    version.string R version 3.6.1 (2019-07-05)’

I think your problem is distinct. Try erasing \freja/homedir$/yundum/Documents/R/win-library/3.6/00LOCK-qiime2R-master/ if it exists and reinstall using devtools::install_github if possible.

2 Likes