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Merged
merged 10 commits into from
Mar 12, 2025
Merged

GitLab CI workflow with sanitizers #6746

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3612a8a
Add the check workflow with sanitizers enabled
aitap Jan 19, 2025
17a6b4f
Try a more R-hub-v2-like approach
aitap Jan 21, 2025
4a7618a
Rewrite action using rocker/r-devel-ubsan-clang
aitap Jan 28, 2025
f218563
Run the sanitizer-enabled checks on GitLab CI
aitap Feb 13, 2025
1585e32
Merge branch 'master' into GHA-sanitizers-rhubv2
aitap Mar 4, 2025
26bfbb3
Update GLCI to use own container image
aitap Mar 4, 2025
577fbac
Remove UBSan suppressions
aitap Mar 6, 2025
0c291b8
Make sure that the *Rout extractor runs too
aitap Mar 6, 2025
9f7b000
Use literal block style to keep newlines intact
aitap Mar 10, 2025
188b171
Merge branch 'master' into GHA-sanitizers-rhubv2
aitap Mar 10, 2025
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1 change: 1 addition & 0 deletions .dev/lsan.supp
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@@ -0,0 +1 @@
leak:libfontconfig.so
2 changes: 2 additions & 0 deletions .dev/ubsan.supp
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# TODO(bit>4.5.0.1): remove after a new 'bit' version is on CRAN
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planning to do that next after data.table release :)

function:R_doDotCall
21 changes: 20 additions & 1 deletion .gitlab-ci.yml
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Expand Up @@ -212,6 +212,25 @@ test-lin-ancient-cran:
# Restore checking vignettes if upgrading our R dependency means knitr can be installed.
- R CMD check --no-manual --no-build-vignettes --ignore-vignettes $(ls -1t data.table_*.tar.gz | head -n 1)

# run the main checks with Address(+Leak),UBSanitizer enabled
test-lin-san:
<<: *test-lin
image: docker.io/rocker/r-devel-ubsan-clang
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is this r-devel-gcc-strict image equivalent?

https://gitlab.com/jangorecki/dockerfiles/-/blame/master/r-devel/r-devel-gcc-strict?ref_type=heads#L43

(thinking it may be preferable to consistently use Jan's repo)

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This way the entire R and (almost) all packages are compiled with -fsanitize=address,undefined. I think there is a way compile just data.table with sanitizers by setting PKG_CFLAGS, PKG_LIBS, but then either the sanitizers must be manually preloaded using LD_PRELOAD or R must be linked with custom MAIN_LD(FLAGS) set.

variables:
# must be set for most of the process because there are pseudo-leaks everywhere
ASAN_OPTIONS: "detect_leaks=0"
# fontconfig is known to leak; add more suppressions as discovered
LSAN_OPTIONS: "suppressions=$CI_PROJECT_DIR/.dev/lsan.supp"
UBSAN_OPTIONS: "suppressions=$CI_PROJECT_DIR/.dev/ubsan.supp"
script:
- ln -svf "$(which RDscript)" "$(which Rscript)" # install-deps will run 'Rscript', we need R-devel+sanitizers
- *install-deps
- >-
ASAN_OPTIONS=detect_leaks=1 RD CMD check --no-manual $(ls -1t data.table_*.tar.gz | head -n 1); res1=$?
perl -nle '(print, $a=1) if /: runtime error: |ERROR: LeakSanitizer/../SUMMARY.*Sanitizer/ }{ exit $a' data.table.Rcheck/**/*.Rout*; res2=$?
# fail if R CMD check had failed or if sanitizer output found
[ $res1 -eq 0 ] && [ $res2 -eq 0 ]

.test-win-template: &test-win
<<: *test
tags:
Expand Down Expand Up @@ -311,7 +330,7 @@ integration:
- saas-linux-medium-amd64
only:
- master
needs: ["mirror-packages","build","test-lin-rel","test-lin-rel-cran","test-lin-dev-gcc-strict-cran","test-lin-dev-clang-cran","test-lin-rel-vanilla","test-lin-ancient-cran","test-win-rel","test-win-dev" ,"test-win-old","test-mac-rel","test-mac-old"]
needs: ["mirror-packages","build","test-lin-rel","test-lin-rel-cran","test-lin-dev-gcc-strict-cran","test-lin-dev-clang-cran","test-lin-rel-vanilla","test-lin-ancient-cran","test-lin-san","test-win-rel","test-win-dev" ,"test-win-old","test-mac-rel","test-mac-old"]
script:
- R --version
- *install-deps ## markdown pkg not present in r-pkgdown image
Expand Down
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