Cannot install qiime2R on R version 3.6.1

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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

3

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

2 Likes
5

Yes, that helped!

Thank you, Best, Agata

6

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)'
7

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
8

Hi Jordan,

I am also having problems installing qiime2R. Could you help me, please?

library (devtools)
Loading required package: usethis
options(download.file.method = "libcurl")
if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
devtools::install_github("jbisanz/qiime2R")
Downloading GitHub repo jbisanz/qiime2R@HEAD
√ checking for file 'C:\Users\Administrator\AppData\Local\Temp\RtmpG8qhBc\remotes45606cff70b2\jbisanz-qiime2R-2db460b/DESCRIPTION' (433ms)

  • preparing 'qiime2R':
    √ checking DESCRIPTION meta-information ...
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • building 'qiime2R_0.99.34.tar.gz'
  • installing source package 'qiime2R' ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Error in inDL(x, as.logical(local), as.logical(now), ...) :
    unable to load shared object 'C:/Program Files/R/R-4.0.0/library/Rcpp/libs/x64/Rcpp.dll':
    LoadLibrary failure: The specified procedure could not be found.
    Calls: ... asNamespace -> loadNamespace -> library.dynam -> dyn.load -> inDL
    Execution halted
    ERROR: lazy loading failed for package 'qiime2R'
  • removing 'C:/Program Files/R/R-4.0.0/library/qiime2R'
    Error: Failed to install 'qiime2R' from GitHub:
    (converted from warning) installation of package ‘C:/Users/ADMINI~1/AppData/Local/Temp/RtmpG8qhBc/file456021ee433f/qiime2R_0.99.34.tar.gz’ had non-zero exit status
9

I suspect your problem is related to Rcpp. Try reinstalling it and then try to install qiime2R.

10

Thanks, Jordan. It was a problem with Rcpp. After updating it, it worked like a charm.
Leo

1 Like
11

Hi Jordan (@jbisanz)

I am facing an error while installing, can you also guide me how to solve the issue;

if (!requireNamespace("devtools", quietly = TRUE)){install.packages("devtools")}
devtools::install_github("jbisanz/qiime2R")
Downloading GitHub repo jbisanz/qiime2R@HEAD
√ checking for file 'C:\Users\DELL 5530\AppData\Local\Temp\Rtmp0aUZPV\remotesd847c7fa6f\jbisanz-qiime2R-2db460b/DESCRIPTION' ...

  • preparing 'qiime2R':
    √ checking DESCRIPTION meta-information ...
  • checking for LF line-endings in source and make files and shell scripts
  • checking for empty or unneeded directories
  • building 'qiime2R_0.99.34.tar.gz'

Installing package into ‘C:/Users/DELL 5530/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)

  • installing source package 'qiime2R' ...
    ** using staged installation
    ** R
    ** inst
    ** byte-compile and prepare package for lazy loading
    Fatal error: cannot open file 'C:\Users\DELL': No such file or directory

ERROR: lazy loading failed for package 'qiime2R'

  • removing 'C:/Users/DELL 5530/Documents/R/win-library/3.6/qiime2R'
    Error: Failed to install 'qiime2R' from GitHub:
    (converted from warning) installation of package ‘C:/Users/DELL 5530/AppData/Local/Temp/Rtmp0aUZPV/filed8416327b3a/qiime2R_0.99.34.tar.gz’ had non-zero exit status

Thank you,

Best,

Eray

12

Strange, I think it is because there is a space in the path to your lib and you are using windows (C:/Users/DELL 5530/Documents/R/win-library/3.6). Possible fixes:
1- try updating to the latest version of devtools
2-download source, and install as I posted here. You may need to manually install the dependencies.
3-move your R libraries to a new directory which avoids ‘DELL 5530’

13

Dear Jordan,

The problem is arisen from the space as you indicated.

Thank you for your time and help.

Best regards,

Eray