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s-u / rJava

R to Java interface
https://RForge.net/rJava
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rjava installation error #289

Closed swati71 closed 2 years ago

swati71 commented 2 years ago

Hello All,

I am trying to install rjava in my linux RedHat8 machine, rstudio. getting the following error. Any help appriciated.

home/isarcu2/softwares/miniconda3/envs/DBT1/bin/../lib/gcc/x86_64-conda-linux-gnu/9.4.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lgomp collect2: error: ld returned 1 exit status make[2]: [Makefile.all:37: libjri.so] Error 1 make[2]: Leaving directory '/tmp/RtmpR5E1Ns/R.INSTALL21e6f8182d1c3f/rJava/jri/src' make[1]: [Makefile.all:19: src/JRI.jar] Error 2 make[1]: Leaving directory '/tmp/RtmpR5E1Ns/R.INSTALL21e6f8182d1c3f/rJava/jri' make: *** [Makevars:14: jri] Error 2 ERROR: compilation failed for package ‘rJava’

The downloaded source packages are in ‘/tmp/RtmpxZ4eRv/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done

s-u commented 2 years ago

Your R does not match the tools on your system so you can't build JRI. You have three options:

swati71 commented 2 years ago

Dear Simon,

Thank you for the response.

Though, I didn't understand the solutions quite well. In your response, you mentioned the package "tools". Are you referring here to 'rtools' ? I downloaded two different versions of R - 4.0.5, and R - 3.2.0, following the instructions given on the following website. https://docs.rstudio.com/resources/install-r/#create-a-symlink-to-r

Can you please elaborate the solution step by step?. I am a newbie in the command line world and have been struggling for many days to resolve this issue.

Hope to hear from you soon.

Thank you

On Mon, Jan 24, 2022 at 2:08 AM Simon Urbanek @.***> wrote:

Your R does not match the tools on your system so you can't build JRI. You have three options:

  • use --disable-jri if you are not using JRI then you only need package tools
  • make sure you use R that you compiled on the system (as opposed to incomplete binaries like the one you have)
  • install the tools that were used to build R that you are using

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s-u commented 2 years ago

@swati71 No, I am talking about compilers and libraries.

First off, if you are not an expert that I assume you don't need JRI so simply use:

install.packages("rJava", repo="https://cran.R-project.org", configure.args="--disable-jri")

if that works, then that's all and ignore anything below.

Since you are using RStudio's special R binaries I would recommend contacting their support as that R is likely incomplete and does not include the necessary tools and libraries. The error above suggests that your R was compiled with GNU OpenMP support and special versions of the GNU compilers which you don't have. It is a very special setup and is incompatible with system R and system tools, so it may take some digging to fix it.