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Published
20 hours ago •
wch
wch
Shadow memory range error with RDsan
This may be related to #24 or #15 . This is the same issue as also reported in coatless-rpkg/sitmo#14
I'm trying to test a different package with RDsan, and I get the following error. Unfortunately, I don't know enough about the C side of things to provide much more information.
To replicate it, I put the following into a Dockerfile and ran docker build -t sitmo-rdsan ..
Dockerfile:
# To build:
# docker build -t sitmo-rdsan .
FROM wch1/r-debug
ENV PKGDEPS="pak::pkg_install('sitmo')"
RUN RDsan -q -e "${PKGDEPS}"
Error:
---> Running in f3da8c62b242
> pak::pkg_install('sitmo')
ℹ Loading metadata database
✔ Loading metadata database ... done
→ Will install 1 package.
→ Will download 1 CRAN package (132.96 kB).
+ sitmo 2.0.2 [bld][cmp][dl] (132.96 kB)
ℹ Getting 1 pkg (132.96 kB)
✔ Got sitmo 2.0.2 (source) (132.96 kB)
ℹ Building sitmo 2.0.2
✖ Failed to build sitmo 2.0.2
Error: <callr_remote_error: Failed to build source package 'sitmo'>
in process 23
-->
Failed to build source package 'sitmo', stdout + stderr:
OE> * installing *source* package ‘sitmo’ ...
OE> ** package ‘sitmo’ successfully unpacked and MD5 sums checked
OE> staged installation is only possible with locking
OE> ** using non-staged installation
OE> ** libs
OE> g++ -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++14 -I"/usr/local/RDsan/lib/R/include" -DNDEBUG -I../inst/include/ -I'/usr/local/RDsan/lib/R/site-library/Rcpp/include' -I/usr/local/include -DSWITCH_TO_REFCNT -fpic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -Wall -Wall -pedantic -Wall -pedantic -c RcppExports.cpp -o RcppExports.o
OE> g++ -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++14 -I"/usr/local/RDsan/lib/R/include" -DNDEBUG -I../inst/include/ -I'/usr/local/RDsan/lib/R/site-library/Rcpp/include' -I/usr/local/include -DSWITCH_TO_REFCNT -fpic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -Wall -Wall -pedantic -Wall -pedantic -c sitmo_demo.cpp -o sitmo_demo.o
OE> g++ -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++14 -I"/usr/local/RDsan/lib/R/include" -DNDEBUG -I../inst/include/ -I'/usr/local/RDsan/lib/R/site-library/Rcpp/include' -I/usr/local/include -DSWITCH_TO_REFCNT -fpic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -Wall -Wall -pedantic -Wall -pedantic -c sitmo_parallel.cpp -o sitmo_parallel.o
OE> g++ -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++14 -I"/usr/local/RDsan/lib/R/include" -DNDEBUG -I../inst/include/ -I'/usr/local/RDsan/lib/R/site-library/Rcpp/include' -I/usr/local/include -DSWITCH_TO_REFCNT -fpic -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O0 -Wall -Wall -pedantic -Wall -pedantic -c sitmo_runif.cpp -o sitmo_runif.o
OE> sitmo_parallel.cpp: In function ‘Rcpp::NumericVector sitmo_parallel(unsigned int, Rcpp::NumericVector&)’:
OE> sitmo_parallel.cpp:37:16: warning: unused variable ‘ncores’ [-Wunused-variable]
OE> 37 | unsigned int ncores = seeds.size();
OE> | ^~~~~~
OE> g++ -fsanitize=address,undefined,bounds-strict -fno-omit-frame-pointer -std=gnu++14 -shared -L/usr/local/RDsan/lib/R/lib -L/usr/local/lib -o sitmo.so RcppExports.o sitmo_demo.o sitmo_parallel.o sitmo_runif.o -L/usr/local/RDsan/lib/R/lib -lRlapack -L/usr/local/RDsan/lib/R/lib -lRblas -L/usr/lib/gcc/x86_64-linux-gnu/9 -lgfortran -lm -lquadmath -L/usr/local/RDsan/lib/R/lib -lR
OE> installing to /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs
OE> ** R
OE> ** inst
OE> ** byte-compile and prepare package for lazy loading
OE> ** help
OE> *** installing help indices
OE> ** building package indices
OE> ** installing vignettes
OE> ** testing if installed package can be loaded
OE> ==101==Shadow memory range interleaves with an existing memory mapping. ASan cannot proceed correctly. ABORTING.
OE> ==101==ASan shadow was supposed to be located in the [0x00007fff7000-0x10007fff7fff] range.
OE> ==101==This might be related to ELF_ET_DYN_BASE change in Linux 4.12.
OE> ==101==See https://github.com/google/sanitizers/issues/856 for possible workarounds.
OE> ==101==Process memory map follows:
OE> 0x00007fff7000-0x00008fff7000
OE> 0x00008fff7000-0x02008fff7000
OE> 0x02008fff7000-0x10007fff8000
OE> 0x5612db615000-0x5612db616000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x5612db616000-0x5612db617000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x5612db617000-0x5612db618000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x5612db618000-0x5612db619000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x5612db619000-0x5612db61a000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x600000000000-0x602000000000
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OE> 0x602000020000-0x602e00000000
OE> 0x602e00000000-0x602e00010000
OE> 0x602e00010000-0x603000000000
OE> 0x603000000000-0x603000020000
OE> 0x603000020000-0x603e00000000
OE> 0x603e00000000-0x603e00010000
OE> 0x603e00010000-0x604000000000
OE> 0x604000000000-0x604000010000
OE> 0x604000010000-0x604e00000000
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OE> 0x615000000000-0x615000060000
OE> 0x615000060000-0x615e00000000
OE> 0x615e00000000-0x615e00010000
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OE> 0x616000000000-0x6160000b0000
OE> 0x6160000b0000-0x616e00000000
OE> 0x616e00000000-0x616e00010000
OE> 0x616e00010000-0x617000000000
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OE> 0x61ee00010000-0x61f000000000
OE> 0x61f000000000-0x61f0000d0000
OE> 0x61f0000d0000-0x61fe00000000
OE> 0x61fe00000000-0x61fe00010000
OE> 0x61fe00010000-0x620000000000
OE> 0x620000000000-0x620000040000
OE> 0x620000040000-0x620e00000000
OE> 0x620e00000000-0x620e00010000
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OE> 0x627000000000-0x627000070000
OE> 0x627000070000-0x627e00000000
OE> 0x627e00000000-0x627e00010000
OE> 0x627e00010000-0x628000000000
OE> 0x628000000000-0x628000050000
OE> 0x628000050000-0x628e00000000
OE> 0x628e00000000-0x628e00010000
OE> 0x628e00010000-0x629000000000
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OE> 0x6290001a0000-0x629e00000000
OE> 0x629e00000000-0x629e00010000
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OE> 0x62a000080000-0x62ae00000000
OE> 0x62ae00000000-0x62ae00010000
OE> 0x62ae00010000-0x62b000000000
OE> 0x62b000000000-0x62b0000b0000
OE> 0x62b0000b0000-0x62be00000000
OE> 0x62be00000000-0x62be00010000
OE> 0x62be00010000-0x62c000000000
OE> 0x62c000000000-0x62c0000c0000
OE> 0x62c0000c0000-0x62ce00000000
OE> 0x62ce00000000-0x62ce00010000
OE> 0x62ce00010000-0x62d000000000
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OE> 0x62de00010000-0x62e000000000
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OE> 0x62ee00000000-0x62ee00010000
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OE> 0x62f000000000-0x62f000060000
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OE> 0x62fe00000000-0x62fe00010000
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OE> 0x640000000000-0x640000003000
OE> 0x7f219755d000-0x7f21978e6000
OE> 0x7f21978e6000-0x7f21978e9000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978e9000-0x7f21978ed000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978ed000-0x7f21978ee000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978ee000-0x7f21978ef000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978ef000-0x7f21978f0000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978f0000-0x7f21978f1000 /usr/lib/x86_64-linux-gnu/librt-2.31.so
OE> 0x7f21978f1000-0x7f2197913000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197913000-0x7f2197a41000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a41000-0x7f2197a76000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a76000-0x7f2197a77000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a77000-0x7f2197a7a000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a7a000-0x7f2197a7d000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a7d000-0x7f2198323000
OE> 0x7f2198323000-0x7f21983dd000 /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs/sitmo.so
OE> 0x7f21983dd000-0x7f219842a000 /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs/sitmo.so
OE> 0x7f219842a000-0x7f2198451000 /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs/sitmo.so
OE> 0x7f2198451000-0x7f2198452000 /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs/sitmo.so
OE> 0x7f2198452000-0x7f219850e000 /tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo/libs/sitmo.so
OE> 0x7f219850e000-0x7f219864a000
OE> 0x7f219864a000-0x7f21988b6000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f21988b6000-0x7f2198a24000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f2198a24000-0x7f2198aaa000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f2198aaa000-0x7f2198aab000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f2198aab000-0x7f2198aad000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f2198aad000-0x7f2198cf3000 /usr/local/RDsan/lib/R/site-library/Rcpp/libs/Rcpp.so
OE> 0x7f2198cf3000-0x7f2198d55000
OE> 0x7f2198d55000-0x7f2198d62000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d62000-0x7f2198d85000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d85000-0x7f2198d90000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d90000-0x7f2198d91000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d91000-0x7f2198d92000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d92000-0x7f2198d9a000 /usr/local/RDsan/lib/R/library/tools/libs/tools.so
OE> 0x7f2198d9a000-0x7f2198fd0000
OE> 0x7f2198fd0000-0x7f2198fd3000 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
OE> 0x7f2198fd3000-0x7f2199000000 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
OE> 0x7f2199000000-0x7f2199018000 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
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OE> 0x7f21992de000-0x7f21992df000 /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0
OE> 0x7f21992df000-0x7f21992e0000 /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0
OE> 0x7f21992e0000-0x7f21992e2000 /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0
OE> 0x7f21992e2000-0x7f21992ec000 /usr/local/RDsan/lib/R/lib/libRlapack.so
OE> 0x7f21992ec000-0x7f2199528000 /usr/local/RDsan/lib/R/lib/libRlapack.so
OE> 0x7f2199528000-0x7f2199530000 /usr/local/RDsan/lib/R/lib/libRlapack.so
OE> 0x7f2199530000-0x7f2199531000 /usr/local/RDsan/lib/R/lib/libRlapack.so
OE> 0x7f2199531000-0x7f2199533000 /usr/local/RDsan/lib/R/lib/libRlapack.so
OE> 0x7f2199533000-0x7f219954d000
OE> 0x7f219954d000-0x7f219956a000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f219956a000-0x7f219965b000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f219965b000-0x7f2199678000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f2199678000-0x7f2199679000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f2199679000-0x7f219967b000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f219967b000-0x7f219968c000 /usr/local/RDsan/lib/R/library/stats/libs/stats.so
OE> 0x7f219968c000-0x7f2199823000
OE> 0x7f2199823000-0x7f2199830000 /usr/local/RDsan/lib/R/library/graphics/libs/graphics.so
OE> 0x7f2199830000-0x7f21998b1000 /usr/local/RDsan/lib/R/library/graphics/libs/graphics.so
OE> 0x7f21998b1000-0x7f21998be000 /usr/local/RDsan/lib/R/library/graphics/libs/graphics.so
OE> 0x7f21998be000-0x7f21998bf000 /usr/local/RDsan/lib/R/library/graphics/libs/graphics.so
OE> 0x7f21998bf000-0x7f21998c7000 /usr/local/RDsan/lib/R/library/graphics/libs/graphics.so
OE> 0x7f21998c7000-0x7f2199924000
OE> 0x7f2199924000-0x7f2199956000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f2199956000-0x7f21999b5000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f21999b5000-0x7f21999e2000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f21999e2000-0x7f21999e3000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f21999e3000-0x7f21999e4000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f21999e4000-0x7f2199a0a000 /usr/local/RDsan/lib/R/library/grDevices/libs/grDevices.so
OE> 0x7f2199a0a000-0x7f2199a59000
OE> 0x7f2199a59000-0x7f2199a5f000 /usr/local/RDsan/lib/R/library/utils/libs/utils.so
OE> 0x7f2199a5f000-0x7f2199a6e000 /usr/local/RDsan/lib/R/library/utils/libs/utils.so
OE> 0x7f2199a6e000-0x7f2199a72000 /usr/local/RDsan/lib/R/library/utils/libs/utils.so
OE> 0x7f2199a72000-0x7f2199a73000 /usr/local/RDsan/lib/R/library/utils/libs/utils.so
OE> 0x7f2199a73000-0x7f2199a76000 /usr/local/RDsan/lib/R/library/utils/libs/utils.so
OE> 0x7f2199a76000-0x7f219a1c4000
OE> 0x7f219a1c4000-0x7f219a1ca000 /usr/local/RDsan/lib/R/library/methods/libs/methods.so
OE> 0x7f219a1ca000-0x7f219a1d1000 /usr/local/RDsan/lib/R/library/methods/libs/methods.so
OE> 0x7f219a1d1000-0x7f219a1d5000 /usr/local/RDsan/lib/R/library/methods/libs/methods.so
OE> 0x7f219a1d5000-0x7f219a1d6000 /usr/local/RDsan/lib/R/library/methods/libs/methods.so
OE> 0x7f219a1d6000-0x7f219a1d9000 /usr/local/RDsan/lib/R/library/methods/libs/methods.so
OE> 0x7f219a1d9000-0x7f219a2f1000
OE> 0x7f219a2f1000-0x7f219a2f4000 /usr/lib/x86_64-linux-gnu/libnss_files-2.31.so
OE> 0x7f219a2f4000-0x7f219a2fb000 /usr/lib/x86_64-linux-gnu/libnss_files-2.31.so
OE> 0x7f219a2fb000-0x7f219a2fd000 /usr/lib/x86_64-linux-gnu/libnss_files-2.31.so
OE> 0x7f219a2fd000-0x7f219a2fe000 /usr/lib/x86_64-linux-gnu/libnss_files-2.31.so
OE> 0x7f219a2fe000-0x7f219a2ff000 /usr/lib/x86_64-linux-gnu/libnss_files-2.31.so
OE> 0x7f219a2ff000-0x7f219a41d000
OE> 0x7f219a41d000-0x7f219a424000 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
OE> 0x7f219a424000-0x7f219a425000 /usr/local/RDsan/lib/R/library/translations/en/LC_MESSAGES/R.mo
OE> 0x7f219a425000-0x7f219a881000
OE> 0x7f219a881000-0x7f219ab67000 /usr/lib/locale/locale-archive
OE> 0x7f219ab67000-0x7f219cbd8000
OE> 0x7f219cbd8000-0x7f219d3b8000
OE> 0x7f219d3b8000-0x7f219d721000
OE> 0x7f219d721000-0x7f219d722000 /usr/lib/x86_64-linux-gnu/libicudata.so.66.1
OE> 0x7f219d722000-0x7f219d723000 /usr/lib/x86_64-linux-gnu/libicudata.so.66.1
OE> 0x7f219d723000-0x7f219f1e0000 /usr/lib/x86_64-linux-gnu/libicudata.so.66.1
OE> 0x7f219f1e0000-0x7f219f1e1000 /usr/lib/x86_64-linux-gnu/libicudata.so.66.1
OE> 0x7f219f1e1000-0x7f219f1e2000 /usr/lib/x86_64-linux-gnu/libicudata.so.66.1
OE> 0x7f219f1e2000-0x7f219f1f0000 /usr/lib/x86_64-linux-gnu/libtinfo.so.6.2
OE> 0x7f219f1f0000-0x7f219f1ff000 /usr/lib/x86_64-linux-gnu/libtinfo.so.6.2
OE> 0x7f219f1ff000-0x7f219f20d000 /usr/lib/x86_64-linux-gnu/libtinfo.so.6.2
OE> 0x7f219f20d000-0x7f219f211000 /usr/lib/x86_64-linux-gnu/libtinfo.so.6.2
OE> 0x7f219f211000-0x7f219f212000 /usr/lib/x86_64-linux-gnu/libtinfo.so.6.2
OE> 0x7f219f212000-0x7f219f214000
OE> 0x7f219f214000-0x7f219f2aa000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f2aa000-0x7f219f39b000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f39b000-0x7f219f3e4000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f3e4000-0x7f219f3e5000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f3e5000-0x7f219f3f0000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f3f0000-0x7f219f3f3000 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.28
OE> 0x7f219f3f3000-0x7f219f3f6000
OE> 0x7f219f3f6000-0x7f219f4df000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f4df000-0x7f219f65c000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f65c000-0x7f219f6e2000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f6e2000-0x7f219f6e3000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f6e3000-0x7f219f6f3000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f6f3000-0x7f219f6f4000 /usr/lib/x86_64-linux-gnu/libicui18n.so.66.1
OE> 0x7f219f6f4000-0x7f219f6f5000
OE> 0x7f219f6f5000-0x7f219f75a000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f75a000-0x7f219f83f000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f83f000-0x7f219f8c5000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f8c5000-0x7f219f8c6000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f8c6000-0x7f219f8d8000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f8d8000-0x7f219f8d9000 /usr/lib/x86_64-linux-gnu/libicuuc.so.66.1
OE> 0x7f219f8d9000-0x7f219f8db000
OE> 0x7f219f8db000-0x7f219f8dd000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8dd000-0x7f219f8ee000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8ee000-0x7f219f8f4000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8f4000-0x7f219f8f5000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8f5000-0x7f219f8f6000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8f6000-0x7f219f8f7000 /usr/lib/x86_64-linux-gnu/libz.so.1.2.11
OE> 0x7f219f8f7000-0x7f219f8f9000 /usr/lib/x86_64-linux-gnu/libbz2.so.1.0.4
OE> 0x7f219f8f9000-0x7f219f906000 /usr/lib/x86_64-linux-gnu/libbz2.so.1.0.4
OE> 0x7f219f906000-0x7f219f908000 /usr/lib/x86_64-linux-gnu/libbz2.so.1.0.4
OE> 0x7f219f908000-0x7f219f909000 /usr/lib/x86_64-linux-gnu/libbz2.so.1.0.4
OE> 0x7f219f909000-0x7f219f90a000 /usr/lib/x86_64-linux-gnu/libbz2.so.1.0.4
OE> 0x7f219f90a000-0x7f219f90c000
OE> 0x7f219f90c000-0x7f219f90f000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f90f000-0x7f219f927000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f927000-0x7f219f932000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f932000-0x7f219f933000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f933000-0x7f219f934000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f934000-0x7f219f935000 /usr/lib/x86_64-linux-gnu/liblzma.so.5.2.4
OE> 0x7f219f935000-0x7f219f937000 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.9.0
OE> 0x7f219f937000-0x7f219f99b000 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.9.0
OE> 0x7f219f99b000-0x7f219f9c3000 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.9.0
OE> 0x7f219f9c3000-0x7f219f9c4000 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.9.0
OE> 0x7f219f9c4000-0x7f219f9c5000 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.9.0
OE> 0x7f219f9c5000-0x7f219f9d9000 /usr/lib/x86_64-linux-gnu/libreadline.so.8.0
OE> 0x7f219f9d9000-0x7f219fa02000 /usr/lib/x86_64-linux-gnu/libreadline.so.8.0
OE> 0x7f219fa02000-0x7f219fa0c000 /usr/lib/x86_64-linux-gnu/libreadline.so.8.0
OE> 0x7f219fa0c000-0x7f219fa0e000 /usr/lib/x86_64-linux-gnu/libreadline.so.8.0
OE> 0x7f219fa0e000-0x7f219fa14000 /usr/lib/x86_64-linux-gnu/libreadline.so.8.0
OE> 0x7f219fa14000-0x7f219fa15000
OE> 0x7f219fa15000-0x7f219fa18000 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
OE> 0x7f219fa18000-0x7f219fa2a000 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
OE> 0x7f219fa2a000-0x7f219fa2e000 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
OE> 0x7f219fa2e000-0x7f219fa2f000 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
OE> 0x7f219fa2f000-0x7f219fa30000 /usr/lib/x86_64-linux-gnu/libgcc_s.so.1
OE> 0x7f219fa30000-0x7f219fa3f000 /usr/lib/x86_64-linux-gnu/libm-2.31.so
OE> 0x7f219fa3f000-0x7f219fae6000 /usr/lib/x86_64-linux-gnu/libm-2.31.so
OE> 0x7f219fae6000-0x7f219fb7d000 /usr/lib/x86_64-linux-gnu/libm-2.31.so
OE> 0x7f219fb7d000-0x7f219fb7e000 /usr/lib/x86_64-linux-gnu/libm-2.31.so
OE> 0x7f219fb7e000-0x7f219fb7f000 /usr/lib/x86_64-linux-gnu/libm-2.31.so
OE> 0x7f219fb7f000-0x7f219fb80000 /usr/lib/x86_64-linux-gnu/libdl-2.31.so
OE> 0x7f219fb80000-0x7f219fb82000 /usr/lib/x86_64-linux-gnu/libdl-2.31.so
OE> 0x7f219fb82000-0x7f219fb83000 /usr/lib/x86_64-linux-gnu/libdl-2.31.so
OE> 0x7f219fb83000-0x7f219fb84000 /usr/lib/x86_64-linux-gnu/libdl-2.31.so
OE> 0x7f219fb84000-0x7f219fb85000 /usr/lib/x86_64-linux-gnu/libdl-2.31.so
OE> 0x7f219fb85000-0x7f219fb87000
OE> 0x7f219fb87000-0x7f219fbac000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fbac000-0x7f219fd24000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fd24000-0x7f219fd6e000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fd6e000-0x7f219fd6f000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fd6f000-0x7f219fd72000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fd72000-0x7f219fd75000 /usr/lib/x86_64-linux-gnu/libc-2.31.so
OE> 0x7f219fd75000-0x7f219fd79000
OE> 0x7f219fd79000-0x7f219fd80000 /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
OE> 0x7f219fd80000-0x7f219fd91000 /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
OE> 0x7f219fd91000-0x7f219fd96000 /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
OE> 0x7f219fd96000-0x7f219fd97000 /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
OE> 0x7f219fd97000-0x7f219fd98000 /usr/lib/x86_64-linux-gnu/libpthread-2.31.so
OE> 0x7f219fd98000-0x7f219fd9c000
OE> 0x7f219fd9c000-0x7f219fda2000 /usr/lib/x86_64-linux-gnu/libubsan.so.1.0.0
OE> 0x7f219fda2000-0x7f219fddc000 /usr/lib/x86_64-linux-gnu/libubsan.so.1.0.0
OE> 0x7f219fddc000-0x7f219fdf2000 /usr/lib/x86_64-linux-gnu/libubsan.so.1.0.0
OE> 0x7f219fdf2000-0x7f219fdf4000 /usr/lib/x86_64-linux-gnu/libubsan.so.1.0.0
OE> 0x7f219fdf4000-0x7f219fdf7000 /usr/lib/x86_64-linux-gnu/libubsan.so.1.0.0
OE> 0x7f219fdf7000-0x7f21a0709000
OE> 0x7f21a0709000-0x7f21a070b000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a070b000-0x7f21a0748000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a0748000-0x7f21a0749000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a0749000-0x7f21a074a000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a074a000-0x7f21a074b000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a074b000-0x7f21a074c000 /usr/local/RDsan/lib/R/lib/libRblas.so
OE> 0x7f21a074c000-0x7f21a088b000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a088b000-0x7f21a0d54000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a0d54000-0x7f21a0e86000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a0e86000-0x7f21a0e87000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a0e87000-0x7f21a0ea4000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a0ea4000-0x7f21a0f68000 /usr/local/RDsan/lib/R/lib/libR.so
OE> 0x7f21a0f68000-0x7f21a10db000
OE> 0x7f21a10db000-0x7f21a10fe000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a10fe000-0x7f21a11cf000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a11cf000-0x7f21a1200000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a1200000-0x7f21a1201000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a1201000-0x7f21a1204000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a1204000-0x7f21a1207000 /usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
OE> 0x7f21a1207000-0x7f21a1aaf000
OE> 0x7f21a1aaf000-0x7f21a1ab0000 /usr/lib/x86_64-linux-gnu/ld-2.31.so
OE> 0x7f21a1ab0000-0x7f21a1ad3000 /usr/lib/x86_64-linux-gnu/ld-2.31.so
OE> 0x7f21a1ad3000-0x7f21a1adb000 /usr/lib/x86_64-linux-gnu/ld-2.31.so
OE> 0x7f21a1adb000-0x7f21a1adc000
OE> 0x7f21a1adc000-0x7f21a1add000 /usr/lib/x86_64-linux-gnu/ld-2.31.so
OE> 0x7f21a1add000-0x7f21a1ade000 /usr/lib/x86_64-linux-gnu/ld-2.31.so
OE> 0x7f21a1ade000-0x7f21a1adf000
OE> 0x7ffd72269000-0x7ffd72306000 [stack]
OE> 0x7ffd7238c000-0x7ffd7238f000 [vvar]
OE> 0x7ffd7238f000-0x7ffd72390000 [vdso]
OE> 0xffffffffff600000-0xffffffffff601000 [vsyscall]
OE> ==101==End of process memory map.
OE> ERROR: loading failed
OE> * removing ‘/tmp/RtmpOd32cX/pkg-lib171e3e4b42/sitmo’
Stack trace:
12. (function (...) ...
13. base:::withCallingHandlers(cli_message = function(msg) { ...
14. get("pkg_install_do_plan", asNamespace("pak"))(...)
15. pkgdepends::install_package_plan(plan = plan, lib = lib, num_workers = num_ ...
16. base:::withCallingHandlers({ ...
17. pkgdepends:::handle_events(state, events)
18. pkgdepends:::handle_event(state, i)
19. pkgdepends:::stop_task(state, worker)
20. pkgdepends:::stop_task_build(state, worker)
21. base:::throw(new_pkg_build_error("Failed to build source package {pkg}", ...
22. base:::signalCondition(cond)
23. (function (e) ...
24. base:::stop(e)
25. (function (e) ...
x Failed to build source package 'sitmo'
Execution halted
While trying to dig a bit deeper (and not really knowing what I'm reading), I found this answer that may be relevant. "If you are using shared ASan DSO, try LD_PRELOAD'ing Asan runtime into your program." at https://github.com/google/sanitizers/wiki/AddressSanitizer#faq
Is that something that could help? Is it something that could be modified in the Makevars or a similar place?
FYI, I tried export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libasan.so.6.0.0 before RUN RDsan -q -e "${PKGDEPS}", and it didn't fix the problem.
And, I tried rebuilding the docker images locally in case there were an architecture issue (I have an AMD processor that I'm using to test it). That also didn't fix the issue.
@billdenney I know you've used a dockerfile, but by exporting LD_PRELOAD in the command line (as you mentioned) worked for me (I had also an issue with lgfortran that I overcame with a symlink),
docker run --rm -ti --security-opt seccomp=unconfined wch1/r-debug
# create symlink for lgfortran
sudo ln -s /usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0 /usr/lib/libgfortran.so
# then export the "libsan"
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libasan.so.6.0.0
RDsan
# then installed required packages (for instance devtools)
install.packages('devtools', dependencies = TRUE, repos = 'https://cloud.r-project.org/')
# and tested code for ASAN
I've also stumbled upon this issue when trying to install igraph using this container. Exporting LD_PRELOAD does not work for libasan.so.6.0.0 or libasan.so.8.0.0. Did you find a different solution @billdenney ?
I did not find a solution yet. (I also haven't tested in a while as my needs are a bit different at the moment.)