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Strengthen CRAN_Release.cmd to find UBSAN errors in data.table.Rcheck #5509

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merged 4 commits into from
Nov 2, 2022
Merged

Strengthen CRAN_Release.cmd to find UBSAN errors in data.table.Rcheck #5509

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eb9a377
interim
mattdowle Oct 30, 2022
6ab71f0
Merge branch 'master' into stderr
mattdowle Nov 1, 2022
6d3905c
remove failed attempts to detect UBSAN errors on stderr
mattdowle Nov 1, 2022
a394725
Add grep of .Rout for UBSAN errors
mattdowle Nov 2, 2022
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33 changes: 22 additions & 11 deletions .dev/CRAN_Release.cmd
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Original file line number Diff line number Diff line change
Expand Up @@ -289,11 +289,11 @@ cd ~/build
wget -N https://stat.ethz.ch/R/daily/R-devel.tar.gz
rm -rf R-devel
rm -rf R-devel-strict-*
tar xvf R-devel.tar.gz
tar xf R-devel.tar.gz
mv R-devel R-devel-strict-gcc
tar xvf R-devel.tar.gz
tar xf R-devel.tar.gz
mv R-devel R-devel-strict-clang
tar xvf R-devel.tar.gz
tar xf R-devel.tar.gz

sudo apt-get -y build-dep r-base
cd R-devel # may be used for revdep testing: .dev/revdep.R.
Expand All @@ -302,8 +302,12 @@ cd R-devel # may be used for revdep testing: .dev/revdep.R.
make

# use latest available `apt-cache search gcc-` or `clang-`
# wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key|sudo apt-key add -
# sudo add-apt-repository 'deb http://apt.llvm.org/jammy/ llvm-toolchain-jammy-15 main'
# sudo apt-get install clang-15

cd ~/build/R-devel-strict-clang
./configure --without-recommended-packages --disable-byte-compiled-packages --enable-strict-barrier --disable-long-double CC="clang-11 -fsanitize=undefined,address -fno-sanitize=float-divide-by-zero -fno-omit-frame-pointer"
./configure --without-recommended-packages --disable-byte-compiled-packages --enable-strict-barrier --disable-long-double CC="clang-15 -fsanitize=undefined,address -fno-sanitize=float-divide-by-zero -fno-sanitize=alignment -fno-omit-frame-pointer" CFLAGS="-g -O3 -Wall -pedantic"
make

cd ~/build/R-devel-strict-gcc
Expand All @@ -329,15 +333,22 @@ alias Rdevel-strict-gcc='~/build/R-devel-strict-gcc/bin/R --vanilla'
alias Rdevel-strict-clang='~/build/R-devel-strict-clang/bin/R --vanilla'

cd ~/GitHub/data.table
Rdevel-strict-gcc CMD INSTALL data.table_1.14.1.tar.gz
Rdevel-strict-clang CMD INSTALL data.table_1.14.1.tar.gz
# Check UBSAN and ASAN flags appear in compiler output above. Rdevel was compiled with them so should be passed through to here
Rdevel-strict-gcc
Rdevel-strict-clang # repeat below with clang and gcc
Rdevel-strict-[gcc|clang] CMD INSTALL data.table_1.14.5.tar.gz
# Check UBSAN and ASAN flags appear in compiler output above. Rdevel was compiled with them so they should be
# passed through to here. However, our configure script seems to get in the way and gets them from {R_HOME}/bin/R
# So I needed to edit my ~/.R/Makevars to get CFLAGS the way I needed.
Rdevel-strict-[gcc|clang] CMD check data.table_1.14.5.tar.gz
# Use the (failed) output to get the list of currently needed packages and install them
Rdevel-strict-[gcc|clang]
isTRUE(.Machine$sizeof.longdouble==0) # check noLD is being tested
options(repos = "http://cloud.r-project.org")
install.packages(c("bit64","xts","nanotime","R.utils","yaml")) # minimum packages needed to not skip any tests in test.data.table()
# install.packages(c("curl","knitr")) # for `R CMD check` when not strict. Too slow to install when strict
install.packages(c("bit64", "bit", "curl", "R.utils", "xts","nanotime", "zoo", "yaml", "knitr", "rmarkdown"))
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maybe set Ncpus if this is really so slow?

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It's not so slow anymore. Didn't time it but under 30 mins I think. Could be that clang's ubsan is faster than gcc's perhaps. I tended to use gcc in the past. Anyway, Ncpus is a good idea, should use it regardless.

# Issue #5491 showed that CRAN is running UBSAN on .Rd examples which found an error so we now run full R CMD check
q("no")
Rdevel-strict-[gcc|clang] CMD check data.table_1.14.5.tar.gz
# UBSAN errors occur on stderr and don't affect R CMD check result. Made many failed attempts to capture them. So grep for them.
find data.table.Rcheck -name "*.Rout" -exec grep -H "runtime error" {} \;

require(data.table)
test.data.table(script="*.Rraw") # 7 mins (vs 1min normally) under UBSAN, ASAN and --strict-barrier
# without the fix in PR#3515, the --disable-long-double lumped into this build does now work and correctly reproduces the noLD problem
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