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RECETOX / recetox-xMSannotator

This is a custom adaptation of the original version of xMSannotator. It is a complete rewrite of the original functionality, following the same program structure.
GNU General Public License v3.0
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Error running covr::codecov in CI #101

Closed xtrojak closed 1 year ago

xtrojak commented 1 year ago

The tests are all passin locally. However, the CI is still failing. The problem can be partially reproduced also locally by running:

Rscript -e "covr::codecov('xmsannotator', quiet = FALSE)"

Giving the following stdout:

Running specific tests for package ‘recetox.xmsannotator’
  Running ‘testthat.R’
'/usr/bin/gcov'  \
  '/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/match_by_mass.gcno'  \
  '-p' '-o' '/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src'

/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/match_by_mass.gcno:version 'B22*', prefer 'A83*'
/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/match_by_mass.gcno:no functions found
/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/match_by_mass.gcda:version 'B22*', prefer version 'A83*'
'/usr/bin/gcov'  \
  '/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/RcppExports.gcno'  \
  '-p' '-o' '/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src'

/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/RcppExports.gcno:version 'B22*', prefer 'A83*'
/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/RcppExports.gcno:no functions found
/m2b/home/trojak/recetox-xMSannotator/xmsannotator/src/RcppExports.gcda:version 'B22*', prefer version 'A83*'
recetox.xmsannotator Coverage: 83.13%
R/compute_confidence_levels.R: 0.00%
R/compute_pathways.R: 0.00%
R/compute_scores.R: 0.00%
R/utils.R: 61.02%
R/compute_peak_modules.R: 61.82%
R/multilevelannotationstep4.R: 69.60%
R/advanced_annotation.R: 78.29%
R/get_confidence_stage2.R: 78.85%
R/get_confidence_stage4.R: 83.41%
R/get_chemscorev1.6.71.R: 88.04%
R/compute_rt_modules.R: 88.10%
R/multilevelannotationstep2.R: 89.04%
R/multilevelannotationstep3.R: 93.68%
R/get_chemscore_october.R: 96.43%
R/group_by_rt_histv2.R: 97.67%
R/compute_isotopes.R: 100.00%
R/group_by_rt.R: 100.00%
R/integration_utils.R: 100.00%
R/multilevelannotationstep5.R: 100.00%
R/simple_annotation.R: 100.00%
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 2.9 seconds...
{html_document}
<html>
[1] <body><p>Could not determine repo and owner</p></body>
Warning message:
In run_gcov(pkg$path, quiet = quiet, clean = clean) :
  parsed gcov output was empty

For CI, however, this leads to Segmentation fault (core dumped).

Originally posted by @xtrojak in https://github.com/RECETOX/recetox-xMSannotator/issues/100#issuecomment-1573287805