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Info

General Process:

Code Block
[salexan5@mblog2 ~]$ cd /project/arcc<project-name>/software/conda-envs/
[salexan5@mblog2 conda-envs]$ module purge
[]$ module load miniconda3/24.3.0
[salexan5@mblog2 conda-envs]$ conda search r-base
Loading channels: done
# Name                       Version           Build  Channel
...
r-base                         4.3.3      hf0d99cb_1  conda-forge
...
r-base                         4.4.1      h1dca405_0  conda-forge
[salexan5@mblog2 conda-envs]$ conda create -p r_4.3.3_env r-base=4.3.3
[salexan5@mblog2 conda-envs]$ conda activate /cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ R --version
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
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(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ R -e 'Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER", "R_LIBS", "R_LIBS_SITE"))'
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> Sys.getenv(c("R_PLATFORM", "R_HOME", "R_LIBS_USER"))
  R_PLATFORM  "x86_64-conda-linux-gnu"
  R_HOME      "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R"
  R_LIBS_USER "/cluster/medbow/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3"
  R_LIBS      ""
  R_LIBS_SITE "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/site-library"

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Code Block
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 ~]$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> .libPaths()
[1] "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library"
Info

Since I own this Conda environment, I have permission to install under: /project/arcc/software/conda-envs/r_4.3.3_env/lib/R.

Lets check:

Code Block
[salexan5@mblog2 ~]$ ls /project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/
base  cli  compiler  datasets  glue  graphics  grDevices  grid  lifecycle  methods  
parallel  rlang  splines  stats  stats4  tcltk  tools  translations  utils  vctrs

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Info

Remember our environment variables:

Code Block
R_LIBS_USER "/cluster/medbow/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3"
R_HOME      "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R"
Code Block
[salexan5@mblog2 ~]$ ls /home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3
ls: cannot access '/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3': No such file or directory
[salexan5@mblog2 ~]$ ls /home/salexan5<username>/R/
x86_64-pc-linux-gnu-library

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Code Block
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 R]$ mkdir -p x86_64-conda-linux-gnu-library/4.3
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 R]$ R
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
...
> .libPaths()
[1] "/cluster/medbow/home/salexan5<username>/R/x86_64-conda-linux-gnu-library/4.3"
[2] "/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library"

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# Within R:
> install.packages("stringi")
...
configure: error: in `/tmp/RtmpVm7ias/R.INSTALL2ad60710733cd2/stringi':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/stringi’

The downloaded source packages are in
        ‘/tmp/Rtmpio5YFH/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("stringi") :
  installation of package ‘stringi’ had non-zero exit status

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Code Block
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda search stringi
Loading channels: done
No match found for: stringi. Search: *stringi*
# Name                       Version           Build  Channel
r-stringi                      0.4_1        r3.1.3_0  pkgs/r
...
r-stringi                      1.8.4   r43hbd1cc82_0  conda-forge

(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda search r-stringi
Loading channels: done
# Name                       Version           Build  Channel
r-stringi                      0.4_1        r3.1.3_0  pkgs/r
...
r-stringi                      1.8.4   r43hbd1cc82_0  conda-forge

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Code Block
(/cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env) [salexan5@mblog2 conda-envs]$ conda install r-stringi
Channels:
 - conda-forge
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##
  environment location: /cluster/medbow/project/arcc<project-name>/software/conda-envs/r_4.3.3_env
  added / updated specs:
    - r-stringi

The following NEW packages will be INSTALLED:
  r-stringi          conda-forge/linux-64::r-stringi-1.8.4-r43hbd1cc82_0
...
Executing transaction: done

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Code Block
[salexan5@mblog2 ~]$ ls /project/arcc<project-name>/software/conda-envs/r_4.3.3_env/lib/R/library/
base  cli  compiler  datasets  glue  graphics  grDevices  grid  lifecycle  methods  parallel  
rlang  splines  stats  stats4  stringi  tcltk  tools  translations  utils  vctrs

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Code Block
conda install -c r r-essentials

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