For posterity: install {xml2} on GNU/Linux distros
This article is originally published at http://www.brodrigues.co/
Today I’ve removed my system’s R package and installed MRO instead. While re-installing all packages, I’ve encountered one of the most frustrating error message for someone installing packages from source:
Error : /tmp/Rtmpw60aCp/R.INSTALL7819efef27e/xml2/man/read_xml.Rd:47: unable to load shared object
'/usr/lib64/R/library/xml2/libs/xml2.so':
libicui18n.so.58: cannot open shared object file: No such file or directory ERROR:
installing Rd objects failed for package ‘xml2’ This library, libicui18n.so.58 is a pain in the butt. However, you can easily install it if you
install miniconda. After installing miniconda, you can look for it with:
[19-05-18 18:26] cbrunos in ~/ ➤ locate libicui18n.so.58
/home/cbrunos/miniconda3/lib/libicui18n.so.58
/home/cbrunos/miniconda3/lib/libicui18n.so.58.2
/home/cbrunos/miniconda3/pkgs/icu-58.2-h9c2bf20_1/lib/libicui18n.so.58
/home/cbrunos/miniconda3/pkgs/icu-58.2-h9c2bf20_1/lib/libicui18n.so.58.2
So now you need to tell R where to look for this library. The
following Stackoverflow answer saved the day. Add the following
lines to R_HOME/etc/ldpaths (in my case, it was in /opt/microsoft/ropen/3.5.2/lib64/R/etc/):
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/miniconda3/lib/
export LD_LIBRARY_PATHand try to install xml2 again, and it should work! If not, just abandon the idea of using R and
switch to doing data science with VBA, it’ll be less frustrating.
Something else, if you install Microsoft R Open, you’ll be stuck with some older packages, because
by default MRO uses a snapshot of CRAN from a given day as a mirror. To get the freshest packages,
add the following line to your .Rprofile file (which should be located in your HOME):
options(repos = c(CRAN = "http://cran.rstudio.com/"))And to finish this short blog post, add the following line to your .Rprofile
if you get the following error messages when trying to install a package from github:
remotes::install_github('rstudio/DT') Downloading GitHub repo rstudio/DT@master tar:
This does not look like a tar archive gzip: stdin: unexpected end of file tar: Child returned
status 1 tar: Error is not recoverable: exiting now tar: This does not look like a tar archive
gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable:
exiting now Error in getrootdir(untar(src, list = TRUE)) : length(file_list) > 0 is not TRUE Calls:
<Anonymous> ... source_pkg -> decompress -> getrootdir -> stopifnot In addition: Warning messages: 1:
In utils::untar(tarfile, ...) : ‘tar -xf '/tmp/RtmpitCFRe/file2677442609b8.tar.gz' -C
'/tmp/RtmpitCFRe/remotes267752f2629f'’ returned error code 2 2:
In system(cmd, intern = TRUE) : running command 'tar -tf '/tmp/RtmpitCFRe/file2677442609b8.tar.gz''
had status 2 Execution haltedThe solution, which can found here
options("download.file.method" = "libcurl")Hope you enjoyed! If you found this blog post useful, you might want to follow me on twitter for blog post updates and buy me an espresso or paypal.me.
Thanks for visiting r-craft.org
This article is originally published at http://www.brodrigues.co/
Please visit source website for post related comments.
