05-06-2023 07:04 PM
When trying to install any of this R libraries from a cmd cell/block on a notebook, or from the UI in the cluster I receive the same error,seeming that are unable to install dependecies.
Warning in utils::install.packages(pkgs, ...) :
installation of package ‘*****’ had non-zero exit status
Can anyone help me with this?
05-16-2023 04:08 PM
For the next soul looking for an answer, I managed to solve the issue with the next 2 Init scripts, it gets tricky in the apt or apt-get, that was the issue, sometimes it did update, sometimes it didn't, making it possible to find libmysqlclient21.
1)
%sh
sudo rm -r /var/lib/apt/lists/*
sudo apt clean &&
sudo apt update --fix-missing -y &&
sudo apt install -y libmysqlclient21
sudo apt install -y gdal-bin
2)
%sh
sudo apt --fix-missing -y update --fix-missing
sudo apt-get install -y libudunits2-dev libproj-dev libgeos-dev libgdal-dev
05-07-2023 12:19 PM
Hi, receiving this message means that the package was not installed. There can be different reasons why this happens, which means there are also different ways to fix this. The most common cause when installing the required package is the existence of unresolved dependencies. Could you please check the same?
Please tag @Debayan with your next comment so that I will get notified. Thank you!
05-07-2023 05:54 PM
Hi @Debayan Mukherjee thanks for your reply, here are my R/Databricks details and the 3 main libraries and errors i am encountering:
platform x86_64-pc-linux-gnu
version.string R version 4.1.3 (2022-03-10)
Runtime
11.3.x-scala2.12
11.3 LTS (includes Apache Spark 3.3.0, Scala 2.12)
gdal
%r
install.packages("gdal", repos = "http://cran.us.r-project.org")
Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08’
(as ‘lib’ is unspecified)
Warning: package ‘gdal’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
terra
%r
install.packages("terra", repos = "http://cran.us.r-project.org")
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++14
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08/terra’
Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08’
(as ‘lib’ is unspecified)
trying URL 'http://cran.us.r-project.org/src/contrib/terra_1.7-29.tar.gz'
Content type 'application/x-gzip' length 806064 bytes (787 KB)
==================================================
downloaded 787 KB
Warning in utils::install.packages(pkgs, ...) :
installation of package ‘terra’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpPqEEXP/downloaded_packages’
raster
%r
install.packages("raster", repos = "http://cran.us.r-project.org")
* installing *source* package ‘terra’ ...
** package ‘terra’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc
configure: CXX: g++ -std=gnu++14
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘terra’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08/terra’
ERROR: dependency ‘terra’ is not available for package ‘raster’
* removing ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08/raster’
Installing package into ‘/local_disk0/.ephemeral_nfs/envs/rEnv-93f5aa20-8204-42c9-b813-cda1cb27ae08’
(as ‘lib’ is unspecified)
also installing the dependency ‘terra’
trying URL 'http://cran.us.r-project.org/src/contrib/terra_1.7-29.tar.gz'
Content type 'application/x-gzip' length 806064 bytes (787 KB)
==================================================
downloaded 787 KB
05-16-2023 04:08 PM
For the next soul looking for an answer, I managed to solve the issue with the next 2 Init scripts, it gets tricky in the apt or apt-get, that was the issue, sometimes it did update, sometimes it didn't, making it possible to find libmysqlclient21.
1)
%sh
sudo rm -r /var/lib/apt/lists/*
sudo apt clean &&
sudo apt update --fix-missing -y &&
sudo apt install -y libmysqlclient21
sudo apt install -y gdal-bin
2)
%sh
sudo apt --fix-missing -y update --fix-missing
sudo apt-get install -y libudunits2-dev libproj-dev libgeos-dev libgdal-dev
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