> 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/DiffBind_3.10.0.tar.gz' Content type 'application/x-gzip' length 6797813 bytes (6.5 MB) ================================================== downloaded 6.5 MB * installing *source* package ‘DiffBind’ ... ** 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 -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c RcppExports.cpp -o RcppExports.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bamReader.cpp -o bamReader.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bam_plbuf.c -o bam_plbuf.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bedReader.cpp -o bedReader.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bitBucket.cpp -o bitBucket.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c croi_func.cpp -o croi_func.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/data/gannet2/ripley/R/test-flang/Rhtslib/include' -I'/data/gannet2/ripley/R/test-flang/Rcpp/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c croi_main.cpp -o croi_main.o In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:962:34: error: too many arguments provided to function-like macro invocation 962 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /data/gannet/ripley/R/R-flang/include/Rinternals.h:968:9: note: macro 'length' defined here 968 | #define length(x) Rf_length(x) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:961:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces 961 | _LIBCPP_INLINE_VISIBILITY | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:758:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY' 758 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:737:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI' 737 | __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER)))) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:962:15: error: expected ';' at end of declaration list 962 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1048:34: error: too many arguments provided to function-like macro invocation 1048 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /data/gannet/ripley/R/R-flang/include/Rinternals.h:968:9: note: macro 'length' defined here 968 | #define length(x) Rf_length(x) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1047:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces 1047 | _LIBCPP_INLINE_VISIBILITY | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:758:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY' 758 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:737:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI' 737 | __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER)))) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1048:15: error: expected ';' at end of declaration list 1048 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1133:34: error: too many arguments provided to function-like macro invocation 1133 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /data/gannet/ripley/R/R-flang/include/Rinternals.h:968:9: note: macro 'length' defined here 968 | #define length(x) Rf_length(x) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1132:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces 1132 | _LIBCPP_INLINE_VISIBILITY | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:758:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY' 758 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:737:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI' 737 | __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER)))) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1133:15: error: expected ';' at end of declaration list 1133 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1309:34: error: too many arguments provided to function-like macro invocation 1309 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ /data/gannet/ripley/R/R-flang/include/Rinternals.h:968:9: note: macro 'length' defined here 968 | #define length(x) Rf_length(x) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1308:5: error: '__abi_tag__' attribute only applies to structs, variables, functions, and namespaces 1308 | _LIBCPP_INLINE_VISIBILITY | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:758:37: note: expanded from macro '_LIBCPP_INLINE_VISIBILITY' 758 | # define _LIBCPP_INLINE_VISIBILITY _LIBCPP_HIDE_FROM_ABI | ^ /usr/local/clang-trunk/bin/../include/c++/v1/__config:737:26: note: expanded from macro '_LIBCPP_HIDE_FROM_ABI' 737 | __attribute__((__abi_tag__(_LIBCPP_TOSTRING(_LIBCPP_VERSIONED_IDENTIFIER)))) | ^ In file included from croi_main.cpp:6: In file included from ./croi_func.h:7: In file included from ./intervalSet.h:4: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/map:2529: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/functional:526: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/__functional/boyer_moore_searcher.h:27: 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: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/locale:202: /usr/local/clang-trunk/bin/../include/c++/v1/__locale:1309:15: error: expected ';' at end of declaration list 1309 | int length(state_type& __st, const extern_type* __frm, const extern_type* __end, size_t __mx) const | ^ 12 errors generated. make: *** [/data/gannet/ripley/R/R-flang/etc/Makeconf:198: croi_main.o] Error 1 ERROR: compilation failed for package ‘DiffBind’ * removing ‘/data/gannet2/ripley/R/test-flang/DiffBind’ * restoring previous ‘/data/gannet2/ripley/R/test-flang/DiffBind’ The downloaded source packages are in ‘/tmp/RtmpyX4AxT/downloaded_packages’ Warning message: In install.packages(foo, configure.args = opts, Ncpus = 25) : installation of package ‘DiffBind’ had non-zero exit status >