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Failed R install package of survminer in Databricks 10.4 LTS

Ross
New Contributor II

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’

1 REPLY 1

shan_chandra
Esteemed Contributor
Esteemed Contributor

@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
%r 
install.packages("survminer")

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