R integration installation fails

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saifr
saifr Registered Posts: 3 ✭✭✭✭

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

Best Answer

  • saifr
    saifr Registered Posts: 3 ✭✭✭✭
    Answer ✓
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    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

Answers

  • fchataigner2
    fchataigner2 Dataiker Posts: 355 Dataiker
    edited July 17
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    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
    saifr Registered Posts: 3 ✭✭✭✭
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    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
    fchataigner2 Dataiker Posts: 355 Dataiker
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    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

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