Add ubsan devcontainer #5850

ben-schwen · 2023-12-21T13:31:38Z

Adds a new clang devcontainer which can be used for checking ubsan errors.
Also sets up the devcontainer to use cc(). For using clang in codespaces, one has to use cc(CC="clang", omp=FALSE).

          Anyone want to have a go at making a UBSAN GitHub Codespace? Would be quite useful.

Originally posted by @MichaelChirico in #5832 (comment)

add symlinks add RUN use echo to create .Rprofile add workdir symlink + echo add dependencies for check add char vec update echo update dockerfile fix FROM update dirs use rocker image rollback to jans clang image change docker order change flags update makevars update flags add workdir change C version clang working rm local .Rprofile

codecov · 2023-12-21T13:42:49Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (6782251) 97.46% compared to head (625022f) 97.46%.
Report is 3 commits behind head on master.

❗ Current head 625022f differs from pull request most recent head 5a7108c. Consider uploading reports for the commit 5a7108c to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #5850   +/-   ##
=======================================
  Coverage   97.46%   97.46%           
=======================================
  Files          80       80           
  Lines       14822    14822           
=======================================
  Hits        14447    14447           
  Misses        375      375

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jangorecki · 2023-12-21T14:18:17Z

.devcontainer/r-devel-clang-ubsan/Dockerfile

+# setup cc()
+WORKDIR /workspaces/data.table
+
+RUN ln -s /workspaces ~/GitHub


What so this one for?

removed for now pending comment

.devcontainer/Dockerfile

.devcontainer/r-devel-clang-ubsan/Dockerfile

MichaelChirico · 2023-12-22T03:33:14Z

.devcontainer/r-devel-clang-ubsan/Dockerfile

+
+# install dependencies without ubsan flags
+RUN Rscript -e '                                          \ 
+read.dcf("DESCRIPTION", c("Imports", "Suggests")) |>      \


{data.table} has very few deps so this is pretty manageable, only takes a few minutes to build.

But for ref. what we've done at {lintr} is specify Config/needs/development with the bare minimum set of packages you'd need to do reasonable development. The idea being if you particularly need vignettes now, you can just install {knitr} yourself from within the container.

Up to us whether we would exclude Suggests by default to get to development faster in the modal case.

I recently pushed to GH related functionality. https://github.com/jangorecki/tools4pkgs/blob/b22666380ec6c675da539e75b49c9fa128718672/R/packages.R#L31

MichaelChirico · 2023-12-22T03:40:26Z

.devcontainer/r-devel-clang-ubsan/Dockerfile

@@ -0,0 +1,23 @@
+FROM registry.gitlab.com/jangorecki/dockerfiles/r-devel-clang


In CRAN_Release.cmd, R itself is specifically configured with the UBSAN options, do we not need that to reproduce the issues?

data.table/.dev/CRAN_Release.cmd

Lines 317 to 319 in 20a43af

cd ~/build/R-devel-strict-clang

./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

Unfortunately while the current setup does appear to pick up the right Makevars for installing {data.table} and gets the .Rprofile correct, it does not appear to reproduce the UBSAN issues mentioned in #5510. Tried with R CMD build . && R CMD check data.table_1.14.99.tar.gz --as-cran (finished with no error).

Possibly R needs to be built with ubsan support. Same as testing for strict barrier. There are some ubsan R docker images online so may be good alternative to use them. I don't think we need ubsan container for codespaces because it is much slower than normal, no? And issues are rather not very frequent.

I've been having a go at re-building a configured R, giving up.

I can get R to build but can't get {data.table} to build:

LLVMSymbolizer: error reading file: No such file or directory ================================================================= ==114458==ERROR: LeakSanitizer: detected memory leaks Direct leak of 6656 byte(s) in 26 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fc72f4 (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x212f4) Direct leak of 1536 byte(s) in 2 object(s) allocated from: #0 0x4ac859 in realloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac859) #1 0x7fe3a7fc73a0 (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x213a0) Direct leak of 16 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fbf491 in FcFontSetCreate (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x19491) #2 0x7fe3a7cff7f3 in Cairo_StrWidth /workspaces/data.table/R-devel/src/library/grDevices/src/cairo/./cairoFns.c:1972:5 #3 0x6ee01b in GEStrWidth /workspaces/data.table/R-devel/src/main/engine.c #4 0x703521 in GEText /workspaces/data.table/R-devel/src/main/engine.c:1887:9 #5 0x7fe3ad10f9ee in Rf_GText /workspaces/data.table/R-devel/src/library/graphics/src/graphics.c:3094:5 #6 0x7fe3ad161a57 in C_title /workspaces/data.table/R-devel/src/library/graphics/src/plot.c:2690:7 #7 0x628874 in do_External /workspaces/data.table/R-devel/src/main/dotcode.c:576:11 #8 0x6837e3 in do_Externalgr /workspaces/data.table/R-devel/src/main/dotcode.c:1626:5 #9 0x746210 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1248:9 #10 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #11 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #12 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #13 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #14 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #15 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #16 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #17 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #18 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #19 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #20 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #21 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #22 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #23 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #24 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #25 0x87eb3a in dispatchMethod /workspaces/data.table/R-devel/src/main/objects.c:472:16 #26 0x87e1d0 in Rf_usemethod /workspaces/data.table/R-devel/src/main/objects.c:522:9 #27 0x87f5f6 in do_usemethod /workspaces/data.table/R-devel/src/main/objects.c:578:9 #28 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #29 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c Direct leak of 16 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fbf491 in FcFontSetCreate (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x19491) #2 0x7fe3a7cfecef in Cairo_MetricInfo /workspaces/data.table/R-devel/src/library/grDevices/src/cairo/./cairoFns.c:1949:5 #3 0x6ed28e in GEMetricInfo /workspaces/data.table/R-devel/src/main/engine.c:2563:2 #4 0x6eeb5d in GEStrHeight /workspaces/data.table/R-devel/src/main/engine.c:2670:2 #5 0x7fe3ad11d214 in Rf_GStrHeight /workspaces/data.table/R-devel/src/library/graphics/src/graphics.c:3072:9 #6 0x7fe3ad14d72d in C_axis /workspaces/data.table/R-devel/src/library/graphics/src/plot.c:1108:20 #7 0x628874 in do_External /workspaces/data.table/R-devel/src/main/dotcode.c:576:11 #8 0x6837e3 in do_Externalgr /workspaces/data.table/R-devel/src/main/dotcode.c:1626:5 #9 0x746210 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1248:9 #10 0x79d1c0 in Rf_evalList /workspaces/data.table/R-devel/src/main/eval.c:3649:12 #11 0x746031 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1239:6 #12 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #13 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #14 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #15 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #16 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #17 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #18 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #19 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #20 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #21 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #22 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #23 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #24 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #25 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #26 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #27 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #28 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #29 0x87eb3a in dispatchMethod /workspaces/data.table/R-devel/src/main/objects.c:472:16 Indirect leak of 663424 byte(s) in 10051 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) Indirect leak of 66608 byte(s) in 181 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0xbc4d38 in _fini (/workspaces/data.table/R-devel/bin/exec/R+0xbc4d38) Indirect leak of 5824 byte(s) in 182 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a8598ac1 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0xcac1) #2 0x62acd1 in R_doDotCall /workspaces/data.table/R-devel/src/main/dotcode.c:866:17 #3 0x682ca4 in do_dotcall /workspaces/data.table/R-devel/src/main/dotcode.c:1552:11 #4 0x746210 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1248:9 #5 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #6 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #7 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #8 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #9 0x79d1c0 in Rf_evalList /workspaces/data.table/R-devel/src/main/eval.c:3649:12 #10 0x746031 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1239:6 #11 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #12 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #13 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #14 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #15 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #16 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #17 0x9d6ed4 in R_DispatchOrEvalSP /workspaces/data.table/R-devel/src/main/subset.c:657:11 #18 0x9d6d69 in do_subset /workspaces/data.table/R-devel/src/main/subset.c:691:8 #19 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #20 0x7affc4 in do_set /workspaces/data.table/R-devel/src/main/eval.c:3551:8 #21 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #22 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #23 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #24 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #25 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #26 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #27 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #28 0x7ab92a in do_if /workspaces/data.table/R-devel/src/main/eval.c:2680:5 #29 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 Indirect leak of 5632 byte(s) in 176 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a8598ac1 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0xcac1) #2 0x62acd1 in R_doDotCall /workspaces/data.table/R-devel/src/main/dotcode.c:866:17 #3 0x682ca4 in do_dotcall /workspaces/data.table/R-devel/src/main/dotcode.c:1552:11 #4 0x746210 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1248:9 #5 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #6 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #7 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #8 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #9 0x79d1c0 in Rf_evalList /workspaces/data.table/R-devel/src/main/eval.c:3649:12 #10 0x746031 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1239:6 #11 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #12 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #13 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c #14 0x79de43 in applyClosure_core /workspaces/data.table/R-devel/src/main/eval.c:2248:16 #15 0x79da32 in Rf_applyClosure /workspaces/data.table/R-devel/src/main/eval.c:2268:16 #16 0x746350 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1268:12 #17 0x9d6ed4 in R_DispatchOrEvalSP /workspaces/data.table/R-devel/src/main/subset.c:657:11 #18 0x9d6d69 in do_subset /workspaces/data.table/R-devel/src/main/subset.c:691:8 #19 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #20 0x79d1c0 in Rf_evalList /workspaces/data.table/R-devel/src/main/eval.c:3649:12 #21 0x746031 in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1239:6 #22 0x7ab92a in do_if /workspaces/data.table/R-devel/src/main/eval.c:2680:5 #23 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #24 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #25 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #26 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #27 0x7aee31 in do_begin /workspaces/data.table/R-devel/src/main/eval.c:2972:10 #28 0x745ebc in Rf_eval /workspaces/data.table/R-devel/src/main/eval.c:1220:12 #29 0x7a881c in R_execClosure /workspaces/data.table/R-devel/src/main/eval.c Indirect leak of 2944 byte(s) in 8 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250028af1af (<unknown module>) Indirect leak of 2944 byte(s) in 8 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62501015c2d7 (<unknown module>) Indirect leak of 2944 byte(s) in 8 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500b8c288f (<unknown module>) Indirect leak of 2576 byte(s) in 7 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625009e84567 (<unknown module>) Indirect leak of 2576 byte(s) in 7 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625010bf63bf (<unknown module>) Indirect leak of 2576 byte(s) in 7 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500faa1de7 (<unknown module>) Indirect leak of 2576 byte(s) in 7 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625000421ac7 (<unknown module>) Indirect leak of 2576 byte(s) in 7 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250113413df (<unknown module>) Indirect leak of 2208 byte(s) in 6 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250112a9ee7 (<unknown module>) Indirect leak of 2208 byte(s) in 6 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500cd2c347 (<unknown module>) Indirect leak of 2208 byte(s) in 6 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625000efc78f (<unknown module>) Indirect leak of 2208 byte(s) in 6 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625008a60737 (<unknown module>) Indirect leak of 2144 byte(s) in 67 object(s) allocated from: #0 0x4ac6b2 in calloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac6b2) #1 0x7fe3a7fc793c (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x2193c) Indirect leak of 1840 byte(s) in 5 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500aa65ad7 (<unknown module>) Indirect leak of 1840 byte(s) in 5 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250112f27ff (<unknown module>) Indirect leak of 1536 byte(s) in 48 object(s) allocated from: #0 0x4ac6b2 in calloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac6b2) #1 0x7fe3a7fc6e0f (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x20e0f) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250106e6dd7 (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250079fc6cf (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500c7d87cf (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500c73ed3f (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250032066af (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250004b7cf7 (<unknown module>) Indirect leak of 1472 byte(s) in 4 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625009e49eff (<unknown module>) Indirect leak of 1104 byte(s) in 3 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500acb60df (<unknown module>) Indirect leak of 1104 byte(s) in 3 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625000fb0fa7 (<unknown module>) Indirect leak of 1104 byte(s) in 3 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250106b2c9f (<unknown module>) Indirect leak of 1104 byte(s) in 3 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500ab89c0f (<unknown module>) Indirect leak of 819 byte(s) in 78 object(s) allocated from: #0 0x497e34 in strdup (/workspaces/data.table/R-devel/bin/exec/R+0x497e34) #1 0x7fe3a7fc6b64 in FcValueSave (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x20b64) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250106b37c7 (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500c882647 (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250110f313f (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250088d39e7 (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625008aa3bb7 (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500cd5e4cf (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500b2414d7 (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500d08586f (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500c76df1f (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625011991e8f (<unknown module>) Indirect leak of 736 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250015ac1ff (<unknown module>) Indirect leak of 512 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fbf567 in FcFontSetAdd (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x19567) Indirect leak of 384 byte(s) in 12 object(s) allocated from: #0 0x4ac6b2 in calloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac6b2) #1 0x7fe3a7fc6cae (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x20cae) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500c763d97 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62501191dcd7 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500fffe0a7 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500a7a214f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625002b678df (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500a96d777 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625001aa4d7f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625011b626af (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500a8f3b47 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625000ea294f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500b970ba7 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x7ffc2fd0124f ([stack]+0xbe24f) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500e17d647 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500e27275f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250015e39df (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500ad758e7 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500ddd7e8f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x6250029e6d07 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500cd1fc5f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625002b669ff (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x625008251057 (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500e239c7f (<unknown module>) Indirect leak of 368 byte(s) in 1 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a859fb78 (/usr/lib/x86_64-linux-gnu/libfreetype.so.6+0x13b78) #2 0x874ffd in HASHTAB /workspaces/data.table/R-devel/src/main/memory.c:4476:37 #3 0x870a4a in CAR0 /workspaces/data.table/R-devel/src/main/memory.c:4311:34 #4 0x62500d6e8837 (<unknown module>) Indirect leak of 128 byte(s) in 4 object(s) allocated from: #0 0x4ac6b2 in calloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac6b2) #1 0x7fe3a7fc6d16 (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x20d16) Indirect leak of 96 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fc0e11 in FcLangSetCreate (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x1ae11) Indirect leak of 48 byte(s) in 2 object(s) allocated from: #0 0x4ac53d in malloc (/workspaces/data.table/R-devel/bin/exec/R+0x4ac53d) #1 0x7fe3a7fc6931 in FcPatternCreate (/usr/lib/x86_64-linux-gnu/libfontconfig.so.1+0x20931) SUMMARY: AddressSanitizer: 820883 byte(s) leaked in 11013 allocation(s).

All of those issues look to be coming from R itself.

I don't think we need ubsan container for codespaces

It's precisely the pain of getting UBSAN right that makes a dedicated codespace attractive. Ideally we can set up the config for it, then run tests there once / cycle.

It's slower than usual, but not painfully (e.g. 10s of minutes to build+test data.table). That's fine for semi-annual testing.

Unfortunately while the current setup does appear to pick up the right Makevars for installing {data.table} and gets the .Rprofile correct, it does not appear to reproduce the UBSAN issues mentioned in #5510. Tried with R CMD build . && R CMD check data.table_1.14.99.tar.gz --as-cran (finished with no error).

Thats what I noticed yesterday and I think the problem is that the issues in #5510 also need ASan and the ASan runtime library is not present in the image (ls /usr/lib/llvm-*/lib/clang/*/lib/linux/libclang_rt.asan-x86_64.a returns nothing).

Hence, why I didn't mark it as finished because I wanted to add the ASan support today :D

https://rocker-project.org/images/base/r-devel.html maybe we just use ubsan image that is already there? assuming it works. It is just once a couple months test that is already mentioned in release procedure.

using rocker/r-devel-ubsan-clang I'm able to reproduce the issues in #5510.
Will update.

Only downside all make calls needs to prepended by LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libasan.so ASAN_OPTIONS='detect_leaks=0:detect_odr_violation=0' e.g. LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libasan.so ASAN_OPTIONS='detect_leaks=0:detect_odr_violation=0' make check

Let's add a README in the folder that includes this step? Or maybe it belongs in CRAN_release (or both)?

I guess both. But I just found out that using RD CMD instead of R work without Makevars and preloading ASAN so I guess remove r-base from the container and linking devel version directly with R is favorable. Will do.

MichaelChirico · 2023-12-22T04:22:28Z

FWIW, here's the CRAN machine configuration that uses some sanitizers:

https://www.stats.ox.ac.uk/pub/bdr/Rconfig/r-devel-linux-x86_64-fedora-gcc

ben-schwen · 2023-12-22T13:14:09Z

Just ran inside devcontainer

make build
LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libasan.so ASAN_OPTIONS='detect_leaks=0:detect_odr_violation=0' make check
find data.table.Rcheck -name "*.Rout" -exec grep -H "runtime error" {} \;

data.table.Rcheck/tests/main.Rout:utils.c:8:38: runtime error: 2.14748e+09 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/main.Rout:gsumm.c:1167:70: runtime error: nan is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1007:21: runtime error: inf is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:900:21: runtime error: -4.61169e+18 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:907:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1024:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'

The errors are the same as in #5510

.devcontainer/r-devel-clang-ubsan/Makevars

MichaelChirico · 2023-12-22T13:27:39Z

Just ran inside devcontainer

make build
LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libasan.so ASAN_OPTIONS='detect_leaks=0:detect_odr_violation=0' make check
find data.table.Rcheck -name "*.Rout" -exec grep -H "runtime error" {} \;

data.table.Rcheck/tests/main.Rout:utils.c:8:38: runtime error: 2.14748e+09 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/main.Rout:gsumm.c:1167:70: runtime error: nan is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1007:21: runtime error: inf is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:900:21: runtime error: -4.61169e+18 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:907:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1024:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'

The errors are the same as in #5510

awesome!! now the $1M question -- does #5832 fix everything?

ben-schwen · 2023-12-22T13:29:32Z

Just ran inside devcontainer

make build
LD_PRELOAD=/usr/lib/gcc/x86_64-linux-gnu/11/libasan.so ASAN_OPTIONS='detect_leaks=0:detect_odr_violation=0' make check
find data.table.Rcheck -name "*.Rout" -exec grep -H "runtime error" {} \;

data.table.Rcheck/tests/main.Rout:utils.c:8:38: runtime error: 2.14748e+09 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/main.Rout:gsumm.c:1167:70: runtime error: nan is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1007:21: runtime error: inf is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:900:21: runtime error: -4.61169e+18 is outside the range of representable values of type 'int'
data.table.Rcheck/tests/nafill.Rout:assign.c:907:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1024:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'

The errors are the same as in #5510

awesome!! now the $1M question -- does #5832 fix everything?

I was running this just now and we still have standing:

data.table.Rcheck/tests/nafill.Rout:assign.c:908:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'
data.table.Rcheck/tests/nafill.Rout:assign.c:1025:21: runtime error: -1.84467e+19 is outside the range of representable values of type 'long'

MichaelChirico · 2023-12-22T13:40:55Z

^ cc @HughParsonage

MichaelChirico · 2023-12-22T14:59:02Z

Merging first. Let's iterate to improve but it'll be easier to use once this is in master & current version is already working.

MichaelChirico

Great work!

ben-schwen and others added 2 commits December 21, 2023 14:27

tidy spaces

ee5fdcb

update flags to #5509

70b0994

jangorecki reviewed Dec 21, 2023

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MichaelChirico reviewed Dec 22, 2023

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MichaelChirico reviewed Dec 22, 2023

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MichaelChirico and others added 6 commits December 22, 2023 10:25

Robust deps install, use files over echo, tidy

caba47f

no ARG

f218b7d

Wrong context?

0072895

need to COPY DESCRIPTION. Try more WORKDIR.

d70e8b5

attempt to fix Makevars, .Rprofile

b78b969

Try copying .Rprofile to /root. Remove ~/GitHub for now.

0808393

MichaelChirico reviewed Dec 22, 2023

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same changes to gcc container

d6d7c06

MichaelChirico reviewed Dec 22, 2023

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MichaelChirico added 3 commits December 22, 2023 03:44

Try adding REdtiorSupport extension by default

e1540b1

load cc conditionally

2007f69

Don't install languageserver by default (slow)

adfa2aa

udpate image and makevars

19b1687

jangorecki reviewed Dec 22, 2023

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drop native

625022f

ben-schwen marked this pull request as ready for review December 22, 2023 13:49

ben-schwen requested a review from mattdowle as a code owner December 22, 2023 13:49

terminal newline

67d2bae

MichaelChirico added 3 commits December 22, 2023 06:49

whitespace

5f00fd1

whitespace

5a7108c

Merge branch 'master' into codespace_devel_clang

4a2a34f

MichaelChirico approved these changes Dec 22, 2023

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MichaelChirico merged commit eace83a into master Dec 22, 2023
2 checks passed

MichaelChirico deleted the codespace_devel_clang branch December 22, 2023 14:59

MichaelChirico mentioned this pull request Dec 22, 2023

Closes #5510: undefined behaviour #5832

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		@@ -0,0 +1,23 @@
		FROM registry.gitlab.com/jangorecki/dockerfiles/r-devel-clang

	cd ~/build/R-devel-strict-clang
	./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

Add ubsan devcontainer #5850

Add ubsan devcontainer #5850

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