> 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/Rsamtools_2.16.0.tar.gz' Content type 'application/x-gzip' length 2918582 bytes (2.8 MB) ================================================== downloaded 2.8 MB * installing *source* package ‘Rsamtools’ ... ** 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 -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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c Biostrings_stubs.c -o Biostrings_stubs.o In file included from Biostrings_stubs.c:1: In file included from /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:1: /data/gannet2/ripley/R/test-flang/Biostrings/include/Biostrings_interface.h:186:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 186 | void drop_reported_matches(); | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/Biostrings_interface.h:188:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 188 | int get_match_count(); | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/Biostrings_interface.h:190:29: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 190 | SEXP reported_matches_asSEXP(); | ^ | void In file included from Biostrings_stubs.c:1: /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:132:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 132 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:19:44: note: expanded from macro 'DEFINE_NOVALUE_CCALLABLE_STUB' 19 | typedef void(*__ ## stubname ## _funtype__)Targs; \ | ^ /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:132:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 132 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:20:15: note: expanded from macro 'DEFINE_NOVALUE_CCALLABLE_STUB' 20 | void stubname Targs \ | ^ /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:137:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 137 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:4:44: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 4 | typedef retT(*__ ## stubname ## _funtype__)Targs; \ | ^ /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:137:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 137 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:5:15: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 5 | retT stubname Targs \ | ^ /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:142:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 142 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:4:44: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 4 | typedef retT(*__ ## stubname ## _funtype__)Targs; \ | ^ /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:142:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 142 | (), | ^ | void /data/gannet2/ripley/R/test-flang/Biostrings/include/_Biostrings_stubs.c:5:15: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 5 | retT stubname Targs \ | ^ 9 warnings generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c IRanges_stubs.c -o IRanges_stubs.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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PileupBuffer.cpp -o PileupBuffer.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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c PosCacheColl.cpp -o PosCacheColl.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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c R_init_Rsamtools.c -o R_init_Rsamtools.o In file included from R_init_Rsamtools.c:4: In file included from ./bamfile.h:6: ./bambuffer.h:14:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 14 | SEXP bambuffer_init(); | ^ | void In file included from R_init_Rsamtools.c:4: In file included from ./bamfile.h:7: ./bam_mate_iter.h:24:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 24 | bam_mates_t *bam_mates_new(); | ^ | void In file included from R_init_Rsamtools.c:4: ./bamfile.h:25:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 25 | SEXP bamfile_init(); | ^ | void In file included from R_init_Rsamtools.c:7: ./io_sam.h:18:22: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 18 | SEXP scan_bam_cleanup(); /* error handling only */ | ^ | void In file included from R_init_Rsamtools.c:8: ./bcffile.h:16:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 16 | SEXP bcffile_init(); | ^ | void In file included from R_init_Rsamtools.c:9: ./fafile.h:13:17: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 13 | SEXP fafile_init(); | ^ | void In file included from R_init_Rsamtools.c:10: ./tabixfile.h:22:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 22 | SEXP tabixfile_init(); | ^ | void 7 warnings generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c ResultManager.cpp -o ResultManager.o ResultManager.cpp:282:13: warning: variable 'i' set but not used [-Wunused-but-set-variable] 282 | int i = 0; | ^ 1 warning generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c S4Vectors_stubs.c -o S4Vectors_stubs.o In file included from S4Vectors_stubs.c:1: In file included from /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:1: /data/gannet2/ripley/R/test-flang/S4Vectors/include/S4Vectors_interface.h:20:23: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 20 | void reset_ovflow_flag(); | ^ | void /data/gannet2/ripley/R/test-flang/S4Vectors/include/S4Vectors_interface.h:22:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 22 | int get_ovflow_flag(); | ^ | void In file included from S4Vectors_stubs.c:1: /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:35:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 35 | (), | ^ | void /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:19:44: note: expanded from macro 'DEFINE_NOVALUE_CCALLABLE_STUB' 19 | typedef void(*__ ## stubname ## _funtype__)Targs; \ | ^ /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:35:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 35 | (), | ^ | void /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:20:15: note: expanded from macro 'DEFINE_NOVALUE_CCALLABLE_STUB' 20 | void stubname Targs \ | ^ /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:40:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 40 | (), | ^ | void /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:4:44: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 4 | typedef retT(*__ ## stubname ## _funtype__)Targs; \ | ^ /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:40:2: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 40 | (), | ^ | void /data/gannet2/ripley/R/test-flang/S4Vectors/include/_S4Vectors_stubs.c:5:15: note: expanded from macro 'DEFINE_CCALLABLE_STUB' 5 | retT stubname Targs \ | ^ 6 warnings generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c XVector_stubs.c -o XVector_stubs.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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c as_bam.c -o as_bam.o In file included from as_bam.c:1: In file included from ./bamfile.h:6: ./bambuffer.h:14:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 14 | SEXP bambuffer_init(); | ^ | void In file included from as_bam.c:1: In file included from ./bamfile.h:7: ./bam_mate_iter.h:24:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 24 | bam_mates_t *bam_mates_new(); | ^ | void In file included from as_bam.c:1: ./bamfile.h:25:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 25 | SEXP bamfile_init(); | ^ | void 3 warnings generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c bam_data.c -o bam_data.o In file included from bam_data.c:2: In file included from ./bamfile.h:6: ./bambuffer.h:14:20: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 14 | SEXP bambuffer_init(); | ^ | void In file included from bam_data.c:2: In file included from ./bamfile.h:7: ./bam_mate_iter.h:24:27: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 24 | bam_mates_t *bam_mates_new(); | ^ | void In file included from bam_data.c:2: ./bamfile.h:25:18: warning: a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes] 25 | SEXP bamfile_init(); | ^ | void 3 warnings generated. /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/S4Vectors/include' -I'/data/gannet2/ripley/R/test-flang/IRanges/include' -I'/data/gannet2/ripley/R/test-flang/XVector/include' -I'/data/gannet2/ripley/R/test-flang/Biostrings/include' -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c bam_mate_iter.cpp -o bam_mate_iter.o In file included from bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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 bam_mate_iter.cpp:2: In file included from ./BamRangeIterator.h:7: In file included from ./BamIterator.h:8: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/set:1761: 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: bam_mate_iter.o] Error 1 ERROR: compilation failed for package ‘Rsamtools’ * removing ‘/data/gannet2/ripley/R/test-flang/Rsamtools’ * restoring previous ‘/data/gannet2/ripley/R/test-flang/Rsamtools’ The downloaded source packages are in ‘/tmp/RtmpjO0lZu/downloaded_packages’ Warning message: In install.packages(foo, configure.args = opts, Ncpus = 25) : installation of package ‘Rsamtools’ had non-zero exit status >