BUG(?): R_LIBS_USER=~/R/%p-library/%v /opt/R/R-latest/bin/Rscript: No such file or directory

[HenrikBengtsson]

@ivan108 reported:

mkdir lg3-demo
cd lg3-demo
lg3 --version
2019-03-23 (commit 749df93)
mkdir output
export PATIENT=Patient157t10
lg3 test setup
*** Setup
[OK] LG3_HOME: /home/shared/cbc/software_cbc/LG3_Pipeline-2019-03-23
/home/shared/cbc/software_cbc/LG3_Pipeline-2019-03-23/bin/lg3-test: line 244: R_LIBS_USER=~/R/%p-library/%v /opt/R/R-latest/bin/Rscript: No such file or directory
[... other tests are OK]]

[HenrikBengtsson]

This is a bug in the sense that:

https://github.com/UCSF-Costello-Lab/LG3_Pipeline/blob/749df93e4060bdc6a1e6f3599da2e24bcc611eee/bin/lg3-test#L244

assumes that the user has already set up a personal R package library at the default location, which all users who run:

> install.packages(...)

at least once and accepts the inquiry by R to create and install to the default user-specific R library path.

[HenrikBengtsson]

Actually, after further investigation, blaming R_LIBS_USER not existing was wrong; that line creates it if it is missing. Instead, I suspect that error:

/home/shared/cbc/software_cbc/LG3_Pipeline-2019-03-23/bin/lg3-test: line 244:
R_LIBS_USER=~/R/%p-library/%v /opt/R/R-latest/bin/Rscript: No such file or directory

is about /opt/R/R-latest/bin/Rscript to being found. I've added an explicit assertion about this before trying to call that Rscript binary, cf. commit 1b1baf64

[HenrikBengtsson]

@ivan108, what machine where you running on for this error to occur?

[ivan108]

I was running on head node from ismirnov account. I tried to re-run lg3 test setup and no errors were detected...

I continue to run test pipeline, currently _run_Recal step. When it is done, I will create empty ./lg3.conf file with single line: PINDEL_NEW=true and see what happens when I run _run_Pindel ...