RomoL2
commented
1 year ago I have installed the RBPamp conda environment (alone and within RegVar) on our cluster so it's working on my linux, but it does look like yours can't find that version of Libgfortran. I will work on streamlining things, but in the meantime you could edit the yml to delete the version requirement on Libgfortran or move it to pip. I am co-opting RBPamp from another member of our lab who wrote it, but it should work without specifying the version.
On Fri, Sep 22, 2023 at 2:01 PM centimorgan22 @.***> wrote:
When trying to install on linux for use in an HPC environment. I get to the step here:
library(RegVar)
install_reqs('/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RegVar')
And then I get this error:
R version 4.2.2 (2022-10-31) -- "Innocent and Trusting" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-conda-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.
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.
library(RegVar) install_reqs('/opt/conda/envs/regvar_env/lib/R/library/RegVar') --2023-09-22 15:09:47-- https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163 Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 983659424 (938M) [application/x-gzip] Saving to: ‘hg38.fa.gz’
hg38.fa.gz 100%[================================================================================================================>] 938.09M 43.0MB/s in 23s
2023-09-22 15:10:10 (41.4 MB/s) - ‘hg38.fa.gz’ saved [983659424/983659424]
- /opt/conda/bin/conda env create --quiet --name 'RBPamp' -f 'environment.yml' Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed
ResolvePackageNotFound:
- libgfortran=5.0.0
Error: Error creating conda environment [exit code 1]
I suspect this has something to do with the way the conda environment specifies the exact version of packages, that may or may not be compatible with both linux & macOS:
For example:
- _r-mutex=1.0.1=anacondar_1
- anyio=3.6.1=py38h50d1736_0
- appnope=0.1.3=pyhd8ed1ab_0
- argon2-cffi=21.3.0=pyhd8ed1ab_0
- argon2-cffi-bindings=21.2.0=py38hed1de0f_2
If possible could you create a docker image for RegVar? This would ensure all users get the same installation environment.
Thank you & interesting paper!
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centimorgan22
apaul7
When trying to install on linux for use in an HPC environment. I get to the step here:
And then I get this error:
I suspect this has something to do with the way the conda environment specifies the exact version of packages, that may or may not be compatible with both linux & macOS:
For example:
If possible could you create a docker image for RegVar? This would ensure all users get the same installation environment.
Thank you & interesting paper!