> install.packages(foo, configure.args = opts, Ncpus = 25) Installing package into ‘/data/gannet2/ripley/R/test-flang’ (as ‘lib’ is unspecified) trying URL 'https://bioconductor.org/packages/3.17/bioc/src/contrib/SeqArray_1.40.1.tar.gz' Content type 'application/x-gzip' length 3591985 bytes (3.4 MB) ================================================== downloaded 3.4 MB * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs using C compiler: ‘clang version 17.0.0 (https://github.com/llvm/llvm-project.git b69d4a4fb707e1623a694d4a2c8fdfa1d8d69a06)’ using C++ compiler: ‘clang version 17.0.0 (https://github.com/llvm/llvm-project.git b69d4a4fb707e1623a694d4a2c8fdfa1d8d69a06)’ /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o In file included from ConvGDS2VCF.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ConvToGDS.cpp -o ConvToGDS.o In file included from ConvToGDS.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o In file included from ConvVCF2GDS.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c FileMerge.cpp -o FileMerge.o In file included from FileMerge.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c GetData.cpp -o GetData.o In file included from GetData.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Index.cpp -o Index.o In file included from Index.cpp:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c LinkSNPRelate.cpp -o LinkSNPRelate.o In file included from LinkSNPRelate.cpp:22: In file included from ./ReadByVariant.h:22: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -DUSING_R -I'/data/gannet2/ripley/R/test-flang/gdsfmt/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c Methods.cpp -o Methods.o In file included from Methods.cpp:24: In file included from ./Index.h:30: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/vector:321: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__format/formatter_bool.h:20: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__format/formatter_integral.h:32: /usr/local/clang-trunk/bin/../include/c++/v1/locale:3642:62: error: no member named 'length' in 'std::char_traits' 3642 | {return from_bytes(__ptr, __ptr + char_traits::length(__ptr));} | ~~~~~~~~~~~~~~~~~~~^ In file included from Methods.cpp:24: ./Index.h:43:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 43 | #define class xclass | ^ ./Index.h:44:9: warning: keyword is hidden by macro definition [-Wkeyword-macro] 44 | #define private xprivate | ^ 2 warnings and 1 error generated. make: *** [/data/gannet/ripley/R/R-flang/etc/Makeconf:198: Methods.o] Error 1 ERROR: compilation failed for package ‘SeqArray’ * removing ‘/data/gannet2/ripley/R/test-flang/SeqArray’ * restoring previous ‘/data/gannet2/ripley/R/test-flang/SeqArray’ The downloaded source packages are in ‘/tmp/RtmpiFaLBy/downloaded_packages’ Warning message: In install.packages(foo, configure.args = opts, Ncpus = 25) : installation of package ‘SeqArray’ had non-zero exit status >