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Home Page: https://hub.docker.com/r/wch1/r-debug
r-debug's Issues
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:
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OE> 0x5612db617000-0x5612db618000 /usr/local/RDsan/lib/R/bin/exec/R
OE> 0x5612db618000-0x5612db619000 /usr/local/RDsan/lib/R/bin/exec/R
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OE> 0x7f219755d000-0x7f21978e6000
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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
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OE> 0x7f2197a7a000-0x7f2197a7d000 /usr/lib/x86_64-linux-gnu/libasan.so.5.0.0
OE> 0x7f2197a7d000-0x7f2198323000
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OE> 0x7f219850e000-0x7f219864a000
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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
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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
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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
Install roxygen2
This is currently necessary to run devtools::test() and devtools::run_examples(). I can do a PR.
New binary for noLD?
First thanks so much for this image. Has proved quite valuable for package dev already on multiple projects.
The last check that's missing (IINM?) is to be able to run tests of a package on a machine without long double support (build option --disable-long-double). rhub has a way to do this but being able to log into an image and do things more interactively is more convenient.
Or if you have a different way that you're doing noLD checks of your packages, would love to hear it.
Need to fix automatic builds on Docker Hub
Automated builds on Docker Hub are no longer working properly. There are two problems that need to be addressed:
- Due to Docker Hub's recent security breach (1, 2), Docker Hub removed its access to my GitHub account. Re-authorizing appears to need read and write access to all of the repositories I have access to, including all the organizations I'm a member of, and I don't think that providing that access is worth the risk.
- Docker Hub's repository links no longer work, so the chained builds do not happen automatically: docker/hub-feedback#1717
Screenshot of the permissions Docker Hub wants:
How to keep in sync with CRAN's settings?
(Not sure this is a valid issue myself so feel free to close)
I once again got a love note from CRAN about UBSAN, and as has happened in the past cannot reproduce. It is a wee bit maddening that they expect us to jump over hoops, but don't really share their rope. Do you have any ideas / plans / suggestions / ... about we could do that better?
(My current case in point is RcppStreams which passes your RDsan and RDcsan yet gets BDR's clang-san to yell at it over some issue deep down in Boost.)
Should use CRAN's config by default?
According to https://svn.r-project.org/R-dev-web/trunk/CRAN/QA/BDR/gannet/R-clang-SAN/config.site this is CRAN's current config for the clang-asan build:
CC="clang -fsanitize=address,undefined -fno-sanitize=float-divide-by-zero -fno-sanitize=alignment -fno-omit-frame-pointer"
OBJC=clang
CXX="clang++ -fsanitize=address,undefined -fno-sanitize=float-divide-by-zero -fno-sanitize=alignment -fno-omit-frame-pointer -frtti"
FC=gfortran
CFLAGS="-g -O3 -Wall -pedantic"
FFLAGS="-g -O2 -mtune=native"
FCFLAGS="-g -O2 -mtune=native"
CXXFLAGS="-g -O3 -Wall -pedantic"
CPPFLAGS="-isystem /usr/local/clang/include"
JAVA_HOME=/usr/lib/jvm/java-1.8.0
LDFLAGS="-L/usr/local/clang/lib64 -L/usr/local/lib64"
MAIN_LD="clang++ -fsanitize=undefined,address"
SHLIB_OPENMP_FFLAGS=
Not everything applies to the Docker image, but some of them are required to reproduce issues on CRAN.
Error installing packages
install.packages("signal")
...
/usr/bin/ld: cannot find -lgfortran
Found solutions here: https://stackoverflow.com/questions/6302209/building-r-package-and-error-ld-cannot-find-lgfortran
Should add rchk
Difference in `NA` behavior with RDvalgrind?
Thank you for this image, it has been invaluable for tracking down errors + run CI with these kinds of debug builds.
I'm debugging some valgrind errors received from CRAN. I've been using the r-debug image to try and recreate the errors, and something that has come up for me is a slight difference in the result of sum(c(1, NA)) under RDvalgrind I get NaN, but under RD I get (what I expect) NA.
I noticed this cause a test that relies on ~sum(c(1, NA)) as an expectation was failing with RDvalgrind on r-debug, though oddly this same test doesn't seem to have failed on CRAN.
docker run --rm -ti wch1/r-debug
root@8f34cb5f5117:/# RDvalgrind -d valgrind -e "sum(c(1, NA))"
==14== Memcheck, a memory error detector
==14== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al.
==14== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info
==14== Command: /usr/local/RDvalgrind/lib/R/bin/exec/R -e sum(c(1,~+~NA))
==14==
R Under development (unstable) (2021-04-27 r80232) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> sum(c(1, NA))
[1] NaN
>
>
==14==
==14== HEAP SUMMARY:
==14== in use at exit: 43,800,695 bytes in 9,574 blocks
==14== total heap usage: 21,780 allocs, 12,206 frees, 67,389,633 bytes allocated
==14==
==14== LEAK SUMMARY:
==14== definitely lost: 0 bytes in 0 blocks
==14== indirectly lost: 0 bytes in 0 blocks
==14== possibly lost: 0 bytes in 0 blocks
==14== still reachable: 43,800,695 bytes in 9,574 blocks
==14== of which reachable via heuristic:
==14== newarray : 4,264 bytes in 1 blocks
==14== suppressed: 0 bytes in 0 blocks
==14== Rerun with --leak-check=full to see details of leaked memory
==14==
==14== For lists of detected and suppressed errors, rerun with: -s
==14== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 0 from 0)
root@8f34cb5f5117:/# RD -e "sum(c(1, NA))"
R Under development (unstable) (2021-04-27 r80232) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> sum(c(1, NA))
[1] NA
>
basic package installation in RDsan is hanging
Please feel free to point out if I am making some fundamentally silly mistake.
docker pull wch1/r-debug:latest
docker run --rm -ti wch1/r-debug:latest bash
RDsan --version gives
R Under development (unstable) (2024-06-05 r86695) -- "Unsuffered Consequences"
running RDsan, then
install.packages("remotes")
The first time I run it I get a huge number of AddressSanitizer:DEADLYSIGNAL errors. (This seems related to this; the fix suggested there (sysctl vm.mmap_rnd_bits=28) returns a "read-only file system" error.
Ctrl-C to quit, then try again:
> install.packages("remotes")
Installing package into ‘/usr/local/RDsan/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/remotes_2.5.0.tar.gz'
Content type 'application/x-gzip' length 164496 bytes (160 KB)
==================================================
downloaded 160 KB
* installing *source* package ‘remotes’ ...
** package ‘remotes’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
At this point the process hangs. As I write this there are two R processes running, one with 7 and one with 9 minutes of accumulated CPU time.
What would the next steps be to diagnose/fix this?
RDsan includes only address sanitizers
I'm guessing this is happening due to a combination of documented difficulties in building R with the GCC UB sanitizer, and the problems caused by ~/.R/Makevars affecting all builds, but the net of it is RDsan does not run the undefined behavior sanitizer. I tried this horrible hack:
echo 'CC=gcc -std=gnu99 -fsanitize=undefined -fno-omit-frame-pointer' > \
~/.R/Makevars &&
RDsan &&
rm ~/.R/Makevars
And was able to get the UB sanitizer to run for RDsan built packages. My shell scripting capabilities are extremely limited, and my R build configuration ones only slightly less so, so I don't have an elegant solution to propose to address this.
Failing a fix, it might be worth updating the documentation to highlight that RDsan, unlike RDcsan, only does address sanitizing for installed packags.
Thanks for this docker container though. It's been a life saver many times.
Docker images no longer updating?
Last build of wch1/r-debug was 2 months ago: https://hub.docker.com/r/wch1/r-devel/
undefined symbol: `__libc_single_threaded`
In the latest build of this image, I am experiencing this error when installing some C++ packages through <Rbuild> CMD INSTALL package.tar.gz:
Error: package or namespace load failed for ‘lightgbm’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/RDvalgrind/lib/R/site-library/00LOCK-lightgbm/00new/lightgbm/libs/lightgbm.so':
/usr/local/RDvalgrind/lib/R/site-library/00LOCK-lightgbm/00new/lightgbm/libs/lightgbm.so: undefined symbol: __libc_single_threaded
Error: loading failed
Execution halted
ERROR: loading failed
Guess it needs to update its libc. Happens with RDcsan too.
Rename R to RR
Starting R with R is now in my muscle memory, I'd rather see an error when starting R in this container instead. Do you see a problem with renaming the executable to RR or anything else?
Don't create so many builds of R
According to @gaborcsardi, only the packages being tested need to be built with instrumentation, not R itself. It would be good to have a mechanism to build packages this way, keeping (roughly) the same user interface.
I know that some R builds are necessary, like RDthreadcheck and RDvalgrind, but it's possible the others do not.
Should use THREADCHECK instead of ASSERT_R_THREAD()
As of
wch/r-source@3c59cea, R itself has a THREADCHECK macro to make sure that various functions are called from the correct thread.
Commit wch/r-source@5cf1f4b also added the checks that were in ASSERT_R_THREAD().
The assertthread build should be changed to use the built-in checks.
Build R in separate directory
The build script should be updated to build R in a separate directory. See: https://github.com/wch/r-source/wiki#building-r-from-source
It sounds like this will require some investigation to figure out how to do it from a git checkout.
ReserveShadowMemoryRange failed
Hello, I am having issue running RDsan.
I started docker as follow:
docker run --rm -ti --security-opt seccomp=unconfined wch1/r-debug
After that, I was able to call RD. But when I called RDsan or RDcsan, I got
root@258bfdfcce6c:/# RDsan
==17==ERROR: AddressSanitizer failed to allocate 0xdfff0001000 (15392894357504) bytes at address 2008fff7000 (errno: 12)
==17==ReserveShadowMemoryRange failed while trying to map 0xdfff0001000 bytes. Perhaps you're using ulimit -v
Aborted (core dumped)
Any suggestions will be appreciated.
Youyi
Request: builds with intel compiler
CRAN has started using the intel compilers in its checks now that it is available free of cost.
Would be nice to have an RD build with the intel compilers.
Compile R with debugging flags
Consider compiling all builds with _GLIBCXX_ASSERTIONS and possibly _GLIBCXX_DEBUG. This will help catch some C++ errors earlier on. (For example, rstudio/httpuv#133.)
https://gcc.gnu.org/onlinedocs/libstdc++/manual/using_macros.html
Note that _GLIBCXX_DEBUG, the documentation says, "this flag changes the sizes and behavior of standard class templates such as std::vector, and therefore you can only link code compiled with debug mode and code compiled without debug mode if no instantiation of a container is passed between the two translation units."
https://gcc.gnu.org/onlinedocs/libstdc++/manual/debug_mode_using.html
-D_GLIBCXX_DEBUG can result in spurious warnings from R CMD check
The various builds of R-devel in this Docker image define -D_GLIBCXX_DEBUG, which defines -D_GLIBCXX_ASSERTIONS, which in turn can cause R CMD check to give spurious warnings about abort and printf. This is the same problem as https://stat.ethz.ch/pipermail/r-package-devel/2018q2/002752.html
It might be necessary to remove -D_GLIBCXX_DEBUG for those warnings to go away.
On the other hand, R itself will need to fix the problem -- otherwise this will be a problem for many packages on Fedora 28.
Daily builds appear to be broken
The README says the following (my emphasis):
... the following Docker images are built daily and pushed to Docker Hub
At https://hub.docker.com/r/wch1/r-debug/tags, it looks like a new image has not been pushed since 2 months ago.
Could you please look into that, and get the builds going again so they keep up with changes to R-devel?
If you could point me at logs or configuration for these builds, I'd be happy to try to help.
Is the use of `Rscript` in `wch1/r-debug` discouraged?
In a project I maintain, we have been using https://hub.docker.com/layers/wch1/r-debug/ for a while now to run various continuous integration jobs trying to replicate the types of testing CRAN does. Thanks so much for maintaining this project!
Starting about 5 days ago, one of those jobs started failing. As of the most recent wch1/r-debug builds, attempting to install {Matrix} from CRAN with Rscript results in the following error.
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
Installing it with RDscript succeeds.
Is the use of Rscript in this image discouraged?
Reproducible Example
This example was run on the latest version of wch1/r-debug:latest, pulled today (May 15, 2021).
output of 'docker inspect' (click me)
Using Rscript, installation of {Matrix} failed.
docker run \
--rm \
--entrypoint="" \
-it wch1/r-debug:latest \
Rscript -e "install.packages('Matrix', repos = 'https://cran.r-project.org')"With this error:
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/usr/local/lib/R/site-library/Matrix’
The downloaded source packages are in
‘/tmp/Rtmps7Wj4h/downloaded_packages’
Warning message:
In install.packages("Matrix", repos = "https://cran.r-project.org") :
installation of package ‘Matrix’ had non-zero exit statu
full log (click me)
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://cran.r-project.org/src/contrib/Matrix_1.4-1.tar.gz'
Content type 'application/x-gzip' length 2862737 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c CHMfactor.c -o CHMfactor.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Csparse.c -o Csparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c TMatrix_as.c -o TMatrix_as.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Tsparse.c -o Tsparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c init.c -o init.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Mutils.c -o Mutils.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c chm_common.c -o chm_common.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cs.c -o cs.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c cs_utils.c -o cs_utils.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dense.c -o dense.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgCMatrix.c -o dgCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgTMatrix.c -o dgTMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dgeMatrix.c -o dgeMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dpoMatrix.c -o dpoMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dppMatrix.c -o dppMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dsCMatrix.c -o dsCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dsyMatrix.c -o dsyMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dspMatrix.c -o dspMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dtCMatrix.c -o dtCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dtTMatrix.c -o dtTMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dtrMatrix.c -o dtrMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dtpMatrix.c -o dtpMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c factorizations.c -o factorizations.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ldense.c -o ldense.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c lgCMatrix.c -o lgCMatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sparseQR.c -o sparseQR.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c abIndex.c -o abIndex.o
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -DUSE_FC_LEN_T -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c packedMatrix.c -o packedMatrix.o
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
( cd Lib ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
( cd Source ; make clean )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
( cd Lib ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_aat.c -o cholmod_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_add.c -o cholmod_add.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_band.c -o cholmod_band.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_common.c -o cholmod_common.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_complex.c -o cholmod_complex.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_copy.c -o cholmod_copy.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_dense.c -o cholmod_dense.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_error.c -o cholmod_error.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_factor.c -o cholmod_factor.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_memory.c -o cholmod_memory.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Core/cholmod_version.c -o cholmod_version.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Check/cholmod_check.c -o cholmod_check.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Check/cholmod_read.c -o cholmod_read.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Check/cholmod_write.c -o cholmod_write.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Modify/cholmod_updown.c -o cholmod_updown.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_aat.c -o cholmod_l_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_add.c -o cholmod_l_add.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_band.c -o cholmod_l_band.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_common.c -o cholmod_l_common.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_complex.c -o cholmod_l_complex.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_copy.c -o cholmod_l_copy.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_dense.c -o cholmod_l_dense.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_error.c -o cholmod_l_error.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_factor.c -o cholmod_l_factor.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_memory.c -o cholmod_l_memory.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Core/cholmod_version.c -o cholmod_l_version.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Check/cholmod_check.c -o cholmod_l_check.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Check/cholmod_read.c -o cholmod_l_read.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Check/cholmod_write.c -o cholmod_l_write.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Modify/cholmod_updown.c -o cholmod_l_updown.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DDLONG -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD/Lib'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/CHOLMOD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c colamd.c -o colamd.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c colamd.c -o colamd_l.o
ar -rucs ../../COLAMD.a colamd.o colamd_l.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/COLAMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
( cd Source ; make -f "/usr/lib/R/etc/Makeconf" -f Makefile lib )
make[2]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_1.c -o amd_i_1.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_2.c -o amd_i_2.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_order.c -o amd_i_order.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_control.c -o amd_i_control.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_info.c -o amd_i_info.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
gcc -I"/usr/share/R/include" -DNDEBUG -I../Include -I../../SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
gcc -I"/usr/share/R/include" -DNDEBUG -DNTIMER -fpic -g -O2 -fdebug-prefix-map=/build/r-base-apO4Ea/r-base-4.2.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpxZGw2m/R.INSTALL1d4ca03978/Matrix/src/SuiteSparse_config'
gcc -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o packedMatrix.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:10: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/usr/local/lib/R/site-library/Matrix’
The downloaded source packages are in
‘/tmp/Rtmps7Wj4h/downloaded_packages’
Warning message:
In install.packages("Matrix", repos = "https://cran.r-project.org") :
installation of package ‘Matrix’ had non-zero exit status
Attempting the same, but with RDscript, succeeds.
docker run \
--rm \
--entrypoint="" \
-it wch1/r-debug:latest \
RDscript -e "install.packages('Matrix', repos = 'https://cran.r-project.org')"* DONE (Matrix)
Notes for Reviewers
According to https://cran.r-project.org/web/packages/Matrix/index.html, {Matrix} was last updated about two months ago (March 23, 2022), so I don't think the root cause of this command starting to fail is "new release of {Matrix}".
I suspect that this issue is related to the way those two executables (R and RD) were built / configured.
docker run \
--rm \
--entrypoint="" \
-it wch1/r-debug \
R CMD config LDFLAGS
# -Wl,-Bsymbolic-functions -Wl,-z,relro
docker run \
--rm \
--entrypoint="" \
-it wch1/r-debug \
RD CMD config LDFLAGS
# -L/usr/local/libThanks very much for your time and consideration.
Rename default branch to main
Taken from rstudio/shiny#3502 (comment)
We're ready to rename master to main here (and elsewhere)!
This blog post announces the larger effort and explains how contributors can update their local environments:
Here's the TL;DR:
- Update usethis (you want usethis v2.1.2 or higher):
install.packages("usethis") - Someone with
adminpermissions on this repo needs to do the renaming,
as I do not have the power:If you wish, you can read the documentation forusethis::git_default_branch_rename()
git_default_branch_rename().
Or do the equivalent from the command line and in the browser (see the blog post). - All remaining contributors can adjust to the renamed default branch with:
If you wish, you can read the documentation for
usethis::git_default_branch_rediscover()
git_default_branch_rediscover().
Or do the command line equivalent (see the blog post).
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