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

[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

[saifr · Accepted solution]

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