> 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/EBImage_4.42.0.tar.gz' Content type 'application/x-gzip' length 5444540 bytes (5.2 MB) ================================================== downloaded 5.2 MB * installing *source* package ‘EBImage’ ... ** 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 -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c EBImage.c -o EBImage.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c clahe.c -o clahe.o clahe.c:223:19: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses] 223 | uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; | ~~~~~~~^~ ~~ clahe.c:223:19: note: place parentheses around the '+' expression to silence this warning 223 | uiSubY = uiYSize+1 >> 1; uiYU = uiNrY-1; uiYB = uiYU; | ^ | ( ) clahe.c:235:23: warning: operator '>>' has lower precedence than '+'; '+' will be evaluated first [-Wshift-op-parentheses] 235 | uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; | ~~~~~~~^~ ~~ clahe.c:235:23: note: place parentheses around the '+' expression to silence this warning 235 | uiSubX = uiXSize+1 >> 1; uiXL = uiNrX - 1; uiXR = uiXL; | ^ | ( ) 2 warnings generated. /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c distmap.cpp -o distmap.o /usr/local/clang-trunk/bin/clang -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c drawCircle.c -o drawCircle.o /usr/local/clang-trunk/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-flang/include" -DNDEBUG -isystem /usr/local/clang-trunk/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -c floodFill.cpp -o floodFill.o In file included from floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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 floodFill.cpp:12: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/stack:128: In file included from /usr/local/clang-trunk/bin/../include/c++/v1/deque:2997: 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: floodFill.o] Error 1 ERROR: compilation failed for package ‘EBImage’ * removing ‘/data/gannet2/ripley/R/test-flang/EBImage’ * restoring previous ‘/data/gannet2/ripley/R/test-flang/EBImage’ The downloaded source packages are in ‘/tmp/RtmpJEk0lR/downloaded_packages’ Warning message: In install.packages(foo, configure.args = opts, Ncpus = 25) : installation of package ‘EBImage’ had non-zero exit status >