Databricks Community

Ross · ‎07-18-2022

I am trying to install the survminer package but I get a non-zero exit status. It may be due to the jpeg package which is a pre-requisite but this also fails when installing independently.

install.packages("survminer", repos = "https://cran.microsoft.com/snapshot/2022-06-24/")

The resulting error is as follows:

* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong  -c bckslv.f -o bckslv.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong  -c chol.f -o chol.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong  -c chol2csr.f -o chol2csr.o
gfortran -fno-optimize-sibling-calls  -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-i2PIHO/r-base-4.1.2=. -fstack-protector-strong  -c cholesky.f -o cholesky.o
cholesky.f:2948:72:
 
.....................
 
Warning in utils::install.packages(pkgs, ...) :
  installation of package ‘jpeg’ had non-zero exit status
Warning in utils::install.packages(pkgs, ...) :
  installation of package ‘gridtext’ had non-zero exit status
Warning in utils::install.packages(pkgs, ...) :
  installation of package ‘ggtext’ had non-zero exit status
Warning in utils::install.packages(pkgs, ...) :
  installation of package ‘survminer’ had non-zero exit status
 
The downloaded source packages are in
	‘/tmp/RtmpugpJqZ/downloaded_packages’

shan_chandra · ‎10-17-2022

@Ross Hamilton - Please follow the below steps in the given order

Run the below init script in an isolated notebook and add the init script to the issue cluster > Advanced options > Init Scripts

%python 
dbutils.fs.put("/tmp/test/init_script.sh","""
#!/bin/bash 
apt-get update
apt-get -y install libjpeg-dev
""")

From CRAN, add the dependent libraries jpeg, gridtext, ggtext to the cluster
add survminer from CRAN to the cluster or use the below command in an isolated notebook attached to the cluster