AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
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Error: install of package 'pd.feinberg.hg18.me.hx1' failed [error code 1] #3221

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

#12 2406.5 Error installing package 'pd.feinberg.hg18.me.hx1':
#12 2406.5 ===================================================
#12 2406.5
#12 2406.5 * installing *source* package ‘pd.feinberg.hg18.me.hx1’ ...
#12 2406.5 ** R
#12 2406.5 ** data
#12 2406.5 ** inst
#12 2406.5 Warning in file.append(to[okay], from[okay]) :
#12 2406.5   write error during file append
#12 2406.5 ** preparing package for lazy loading
#12 2406.5 ** help
#12 2406.5 Error : /tmp/Rtmpm0pEMa/R.INSTALL72043adf6a7b/pd.feinberg.hg18.me.hx1/man/pkg.Rd: Sections \title, and \name must exist and be unique in Rd files
#12 2406.5 ERROR: installing Rd objects failed for package ‘pd.feinberg.hg18.me.hx1’
#12 2406.5 * removing ‘/usr/local/lib/R/site-library/.renv/1/pd.feinberg.hg18.me.hx1’
#12 2406.5 Error: install of package 'pd.feinberg.hg18.me.hx1' failed [error code 1]
#12 2406.5 Traceback (most recent calls last):
#12 2406.5 12: renv::restore(prompt = FALSE, rebuild = TRUE)
#12 2406.5 11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
#12 2406.5 10: renv_install_impl(records)
#12 2406.5  9: renv_install_staged(records)
#12 2406.5  8: renv_install_default(records)
#12 2406.5  7: handler(package, renv_install_package(record))
#12 2406.5  6: renv_install_package(record)
#12 2406.5  5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
#12 2406.5         vwritef("\tFAILED")
#12 2406.5         writef(e$output)
#12 2406.5     })
#12 2406.5  4: renv_install_package_impl(record)
#12 2406.5  3: r_cmd_install(package, path)
#12 2406.5  2: r_exec_error(package, output, "install", status)
#12 2406.5  1: stop(error)
#12 2407.0 Execution halted
#12 ERROR: process "/bin/bash -o pipefail -c Rscript renv_load.R" did not complete successfully: exit code: 1

Solution or next step

Troubleshoot and fix the R exception.

arkid15r commented 1 year ago

It appeared to be transient as it's gone within next rebuild attempt.