Difficulty configuring/installing R on mox

[yaaminiv]

I am following these instructions to get the latest version of R on mox using source code (The UC Berkeley CRAN mirror link is defunct, so I am using one from OSU).

I'm on step 9, configuration/installation:

When I try running the configure command, I get the following error:

Is there something I'm missing?

[sr320]

feels like you are in wrong directory... see step 7?

[kubu4]

If you're following those instructions exactly, you need to be in the Rstuff directory you created in Step 2.

Basically, I suspect you're in the wrong directory. You need to be in the same directory in which you downloaded the R*.gz file.

[kubu4]

And then, like @sr320 points out, you need to change in to the directory created in Step 7.

[yaaminiv]

yup, I was in the wrong directory!

I forgot that I was unable to download into the Rstuff directory so I downloaded it into my user directory, then navigated out back into the wrong directory when I did step 8

[yaaminiv]

Okay, new question!

I ran ./configure --prefix=/gscratch/srlab/yaaminiv/Rinstall from the R-4.0.5 directory. The R-4.0.5 directory is NOT in Rstuff, but in my user directory. I got the following error:

configure: error: PCRE2 library and headers are required, or use --with-pcre1 and PCRE >= 8.32 with UTF-8 support

A quick search lead me to this page, so I think I need to install this package? However, I was looking through the R installation instructions again, and I saw that having anaconda python would prevent successful installation.

How do I remove anaconda python from my path? I'm looking at my ~/.bashrc profile...do I just delete export PATH="/usr/lusers/yaaminiv/miniconda3/bin:$PATH?

edited to include full error message

[kubu4]

Okay, if you want to follow the suggestions in those instructions you posted above, I'd comment out all of that conda initialize section. Don't delete anything, though. After commenting stuff out, follow the rest of the instructions regarding logging out, etc.

[yaaminiv]

Whoops, just edited to include the full error message.

Tried ./configure --prefix=/gscratch/srlab/yaaminiv/Rinstall --with-prce1 and got the same error message.

[yaaminiv]

• Commented out conda initialize section
• Logged out and requested a new build node
• Ran ./configure --prefix=/gscratch/srlab/yaaminiv/Rinstall, same error
• Ran ./configure --prefix=/gscratch/srlab/yaaminiv/Rinstall --with-prce1successfully (I think!)! Got some warnings:

• Ran make with no error
• Ran make install, ended up with disk quota error.

How do I get more disk space? I only have R installation stuff + miniconda in my user directory.

[kubu4]

You can't get more space on your login node. That's why we have the programs directory in the /gscratch/srlab/programs/.

However, we're also over quota there... Have deleted some stuff, but takes time to update the system.

[yaaminiv]

You can't get more space on your login node. That's why we have the programs directory in the /gscratch/srlab/programs/.

It's installing at /gscratch/srlab/yaaminiv/Rinstall/, not my login node! So at least that's good.

However, we're also over quota there... Have deleted some stuff, but takes time to update the system.

I'll wait and see if I can try installing again.

[sr320]

I might be missing something but cannot you just load the module...
partial list of what is available

r_3.3.3                                                      
r_3.5.1                                                      
r_3.6.0                                                      
r_3.6.0+Rmpi-impi_2019   

you are installing from source (which might not be necessary?)

[kubu4]

I think she wanted a newer version, as we also have /gscratch/srlab/programs/R-3.6.2/

[sr320]

OK
FWIW this works

[sr320@n2193 R]$ module load r_3.6.0
[sr320@n2193 R]$ module list
Currently Loaded Modulefiles:
 1) icc_19   2) r_3.6.0  
[sr320@n2193 R]$ R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 

[yaaminiv]

@sr320 I wanted the newest version of R (if possible)! I'll see if dealing with conda lets me load R-4.0.5, and if not, I'll test the workflow with the versions of R we already have installed

[yaaminiv]

Success!!

Tips in case anyone has to do this again......

• use python, not anaconda python
• download R to user directory and configure/make/install in /gscratch/srlab/YOURDIRECTORY/Rinstall
• make sure there is enough disk space