R integration installation fails

saifr

Hi,

I have been trying to run (and re-run) the R_integration script on Ubuntu (via WSL on Windows), and it keeps failing. Welcome your advice/help please. Thanks

** checking absolute paths in shared objects and dynamic libraries
mv: cannot move '/home/saifr/configData/R.lib/00LOCK-xml2/00new/xml2' to '/home/saifr/configData/R.lib/xml2': Permission denied
ERROR: moving to final location failed
ERROR: dependency ‘xml2’ is not available for package ‘sparklyr’
* removing ‘/home/saifr/configData/R.lib/sparklyr’

The downloaded source packages are in
‘/tmp/RtmpRAVrCe/downloaded_packages’
Checking installed packages ...
Package not installed: sparklyr
Error: at least one package failed to install required version
In addition: Warning messages:
1: In install.packages(toInstall, "/home/saifr/configData/R.lib", repos = "https://cloud.r-project.org") :
installation of package ‘xml2’ had non-zero exit status
2: In install.packages(toInstall, "/home/saifr/configData/R.lib", repos = "https://cloud.r-project.org") :
installation of package ‘sparklyr’ had non-zero exit status
Execution halted

saifr

Frederic @fchataigner2
, hi,

No worries. Just to update you I have not followed your latest suggestion only because updating WSL to WSL 2 fixed the issue. It would seem the "mv" semantics are/were not correct in WSL, which appears to have been addressed in WSL 2.

Thanks again

fchataigner2

Hi,

this error typically means you haven't installed the xml2 system package on the machine. On a vanilla Ubuntu, you'd solve that with

apt-get install libxml2-dev

so if WSL works as I imagine, it should work in your case too.

Regards,

Frederic

saifr

Hi Frederic @fchataigner2
,

Thank you for your suggestion. I had already done that "apt-get install libxml2-dev".

It is while running the R integration script that it fails, trying to move the "xml2 file", and halts the execution.

Welcome any other thoughts. Thanks

fchataigner2

Hi,

apologies, I read the R log too fast. Indeed your R.lib contains a botched up xml2 install (or a failed uninstall, that happens sometimes). You can try to clean this up with remove.packages("xml2", "/home/saifr/configData/R.lib"), or manually by removing traces of xml2 in /home/saifr/configData/R.lib, but IIRC the only safe method is to just trash the contents of /home/saifr/configData/R.lib and start again...

Regards,

Frederic