Source: trinityrnaseq Version: 2.11.0+dfsg-6 Severity: serious Tags: sid bullseye X-Debbugs-CC: debian...@lists.debian.org User: debian...@lists.debian.org Usertags: flaky
Dear maintainer(s), Your package has an autopkgtest, great. However, I looked into the history of your autopkgtest [1] on amd64 and arm64 (because it is blocking perl) and I noticed it fails regularly, while a rerun passes. I copied some of the output at the bottom of this report. The last warning has a different number every time. Because the unstable-to-testing migration software now blocks on regressions in testing, flaky tests, i.e. tests that flip between passing and failing without changes to the list of installed packages, are causing people unrelated to your package to spend time on these tests. Please do get in touch if we need to dive into this together. Or if you want to discuss this issue. I noticed that all the failed runs I checked were done on the same worker. Could the problem be a timing issue? (The worker has a spinning disk and is slower than our other workers). Paul https://ci.debian.net/data/autopkgtest/testing/arm64/t/trinityrnaseq/10170685/log.gz https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/10058739/log.gz https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/10172707/log.gz https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/10194744/log.gz https://ci.debian.net/data/autopkgtest/testing/amd64/t/trinityrnaseq/10216335/log.gz Warning messages: 1: Removed 55 rows containing missing values (geom_point). 2: Removed 1 rows containing missing values (geom_text). GOBubble, bckgrd color Warning messages: 1: Removed 55 rows containing missing values (geom_point). 2: Removed 1 rows containing missing values (geom_text). GOCircle Error: Breaks and labels are different lengths Backtrace: █ 1. └─GOplot::GOCircle(circ) 2. └─gridExtra::grid.arrange(c, table, ncol = 2) 3. └─gridExtra::arrangeGrob(...) 4. └─base::lapply(grobs[toconv], ggplot2::ggplotGrob) 5. └─ggplot2:::FUN(X[[i]], ...) 6. ├─ggplot2::ggplot_gtable(ggplot_build(x)) 7. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x)) 8. └─ggplot2:::build_guides(...) 9. └─ggplot2:::guides_train(...) 10. ├─ggplot2::guide_train(guide, scale, output) 11. └─ggplot2:::guide_train.colorbar(guide, scale, output) 12. └─scale$get_labels(breaks) 13. └─ggplot2:::f(..., self = self) Warning messages: 1: Removed 6 rows containing missing values (geom_point). 2: Removed 6 rows containing missing values (geom_point). Execution halted Error, CMD: /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/GOplot.Rscript --EC_david ./EC.david --EC_genelist ./EC.genelist --pdf_outfile goplot.pdf died with ret 256 at /usr/lib/trinityrnaseq/Analysis/DifferentialExpression/prep_n_run_GOplot.pl line 246. make[1]: *** [Makefile:4: test] Error 25 make[1]: Leaving directory '/tmp/autopkgtest-lxc.9tclu2at/downtmp/autopkgtest_tmp/trinityrnaseq/trinity_ext_sample_data/test_GOplot' make: *** [Makefile:18: test] Error 2 autopkgtest [00:08:05]: test run-tests: -----------------------]
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