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
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.
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
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
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'