Errors while running circtools_install_R_dependencies

[shubhada-kulkarni]

Dear Tobias,

I am trying to install the latest circtools installation and I managed to do it using pip install. However, when I try to install the R packages using circtools_install_R_dependencies script, I get error related to installation of primex package. The error message is attached below. I am using R version 4.2.1.

(base) skulkarni@slurm-c-mk1-5c:/prj/circtools2/installation$ circtools_install_R_dependencies 

This script will automatically install R packages required by circtools.

Detected R version 4.2.1

Detected library paths:
-> /beegfs/homes/skulkarni
-> /beegfs/biosw/R/4.2.1_deb11/lib/R/library

Need to install package aod
Need to install package amap
Need to install package ballgown
Need to install package biomaRt
Need to install package edgeR
Need to install package GenomicFeatures
Need to install package GenomicRanges
Need to install package ggbio
Need to install package ggfortify
Need to install package gplots
Need to install package ggrepel
Need to install package gridExtra
Need to install package openxlsx
Need to install package plyr
Need to install package Hmisc
Need to install package reshape2
Need to install package kableExtra
Need to install package formattable

Installation will start in 10 seconds.
Press ctrl+c to cancel.

 0
Now installing R CircTest and primex R packages.

Installing package into ‘/beegfs/homes/skulkarni’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘GenomicRanges’, ‘BSgenome’, ‘IRanges’, ‘S4Vectors’, ‘Biostrings’ are not available for package ‘primex’
* removing ‘/beegfs/homes/skulkarni/primex’
Warning message:
In install.packages(paste0(base_path, "/contrib/primex"), repos = NULL,  :
  installation of package ‘/home/skulkarni/.local/lib/python3.10/site-packages/circtools/contrib/primex’ had non-zero exit status
Installing package into ‘/beegfs/homes/skulkarni’
(as ‘lib’ is unspecified)
ERROR: dependencies ‘aod’, ‘plyr’ are not available for package ‘CircTest’
* removing ‘/beegfs/homes/skulkarni/CircTest’
Warning message:
In install.packages(paste0(base_path, "/contrib/circtest"), repos = NULL,  :
  installation of package ‘/home/skulkarni/.local/lib/python3.10/site-packages/circtools/contrib/circtest’ had non-zero exit status

[tjakobi]

Hi @shubhada-kulkarni ,

Just to make sure, how did you install circtools using pip? From pypi or directly from the git repository?

I added a fix in the master branch of this repository, please pull the latest changes and retry the installation.

Best,

Tobias

[shubhada-kulkarni]

Hello @tjakobi,

I first installed using pypi, which is when I got this error. Later I tried with git and I got the same error again.

Now I tried after pulling the latest changes, I still have the same errors. The circtools installation went okay, but installing R packages is giving errors related to dependencies. Please see both output for both commands (python setup.py install and circtools_install_R_dependencies) in attach.

Regards, Shubhada output_circtools2_installation_git_300723.txt output_circtools2_installation_R_300723.txt

[tjakobi]

Thank you for the report @shubhada-kulkarni. It seems Microsoft retired their CRAN mirror that the script was using, which made the installation fail. I removed the hard-coded references to the mirrors and we now only use the default mirrors.

Please pull the repository and re-try the installation.

[shubhada-kulkarni]

Unfortunately, that did not work either. Is there anything else that I should check from my side that might be causing this problem?

Please find the command output in attach. output_circtools2_installation_R_020823.txt

[tjakobi]

You are still using the old code, not the fixed version. Did you perform a git pull of this repository before attempting installation?

[shubhada-kulkarni]

I did git clone before trying the installation. But now just to make sure, I removed all previous installations and retried using pip install git+https://github.com/jakobilab/circtools.git --user and it worked. Please find the command report attached. Thanks! output_circtools2_installation_030823.txt

[tjakobi]

git commit commits your changes to the branch/repository. You need to use git pull to retrieve the remote changes.

Closing this issues since it has been solved.

[shubhada-kulkarni]

My apologies, I wanted to say git clone and not git commit.

[tjakobi]

Hi @shubhada-kulkarni,

with git clone you are creating an entire new copy of a remote repository, which is not what you usually want, specifically if there might be local changes that you will otherwise overwrite. git pull will retrieve changes into an already cloned repository.

For the general git workflow see the extensive introduction of GitHub: https://docs.github.com/en/get-started/using-git/about-git