* installing *source* package ‘XYomics’ ... ** this is package ‘XYomics’ version ‘0.1.5’ ** package ‘XYomics’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C++ compiler: ‘Apple clang version 21.0.0 (clang-2100.1.1.101)’ using SDK: ‘MacOSX26.5.sdk’ clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/Rcpp/include' -I'/Users/ripley/R/Library/BH/include' -isystem /opt/R/arm64/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c PCSF.cpp -o PCSF.o In file included from PCSF.cpp:8: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:79: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/sugar.h:33: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/functions.h:63: /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:38:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 38 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:44:20: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 44 | s += t/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:68:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 68 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:69:15: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 69 | si /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:77:20: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 77 | s += t/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:78:22: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 78 | si += ti/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:104:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 104 | s /= n; // no overflow correction needed for logical vectors | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:122:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 122 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:128:16: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 128 | s += t/n; | ~^ In file included from PCSF.cpp:8: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:93: /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:399:14: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 399 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:407:22: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 407 | s += t / n; | ~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:426:14: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 426 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:435:22: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 435 | s += t / n; | ~ ^ In file included from PCSF.cpp:14: In file included from /Users/ripley/R/Library/BH/include/boost/random.hpp:66: /Users/ripley/R/Library/BH/include/boost/random/discrete_distribution.hpp:285:44: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'double' may lose precision [-Wimplicit-int-float-conversion] 285 | double delta = (xmax - xmin) / n; | ~ ^ /Users/ripley/R/Library/BH/include/boost/random/discrete_distribution.hpp:404:40: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'double' may lose precision [-Wimplicit-int-float-conversion] 404 | double delta = (xmax - xmin) / n; | ~ ^ In file included from PCSF.cpp:8: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27: In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:30: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/r/headers.h:67: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/platform/compiler.h:39: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:605: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:22: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:1439: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwd:112: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/fstream.h:13: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/string.h:45:41: warning: 'char_traits' is deprecated: char_traits for T not equal to char, wchar_t, char8_t, char16_t or char32_t is non-standard and is provided for a temporary period. It will be removed in a future release, so please migrate off of it. [-Wdeprecated-declarations] 45 | template , class _Allocator = allocator<_CharT> > | ^ /Users/ripley/R/Library/BH/include/boost/xpressive/traits/cpp_regex_traits.hpp:321:18: note: in instantiation of default argument for 'basic_string' required here 321 | typedef std::basic_string string_type; | ^~~~~~~~~~~~~~~~~~~~~~~ /Users/ripley/R/Library/BH/include/boost/xpressive/traits/cpp_regex_traits.hpp:673:22: note: in instantiation of template class 'boost::xpressive::cpp_regex_traits' requested here 673 | inline unsigned char cpp_regex_traits::hash(unsigned char ch) | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/string.h:24:8: note: 'char_traits' has been explicitly marked deprecated here 24 | struct _LIBCPP_DEPRECATED_( | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:555:53: note: expanded from macro '_LIBCPP_DEPRECATED_' 555 | # define _LIBCPP_DEPRECATED_(m) __attribute__((__deprecated__(m))) | ^ In file included from PCSF.cpp:8: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:27: In file included from /Users/ripley/R/Library/Rcpp/include/RcppCommon.h:30: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/r/headers.h:67: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/platform/compiler.h:39: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/unordered_map:605: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__memory_resource/polymorphic_allocator.h:22: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:1439: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iosfwd:112: In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/fstream.h:13: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/string.h:45:41: warning: 'char_traits' is deprecated: char_traits for T not equal to char, wchar_t, char8_t, char16_t or char32_t is non-standard and is provided for a temporary period. It will be removed in a future release, so please migrate off of it. [-Wdeprecated-declarations] 45 | template , class _Allocator = allocator<_CharT> > | ^ /Users/ripley/R/Library/BH/include/boost/xpressive/traits/cpp_regex_traits.hpp:321:18: note: in instantiation of default argument for 'basic_string' required here 321 | typedef std::basic_string string_type; | ^~~~~~~~~~~~~~~~~~~~~~~ /Users/ripley/R/Library/BH/include/boost/xpressive/traits/cpp_regex_traits.hpp:685:22: note: in instantiation of template class 'boost::xpressive::cpp_regex_traits' requested here 685 | inline unsigned char cpp_regex_traits::hash(signed char ch) | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__fwd/string.h:24:8: note: 'char_traits' has been explicitly marked deprecated here 24 | struct _LIBCPP_DEPRECATED_( | ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__config:555:53: note: expanded from macro '_LIBCPP_DEPRECATED_' 555 | # define _LIBCPP_DEPRECATED_(m) __attribute__((__deprecated__(m))) | ^ PCSF.cpp:104:24: warning: implicit conversion loses integer precision: 'typename config::vertex_descriptor' (aka 'unsigned long') to 'mapped_type' (aka 'int') [-Wshorten-64-to-32] 104 | return g_map[id] = add_vertex(VertexProperties(id), g); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:111:24: warning: implicit conversion loses integer precision: 'typename config::vertex_descriptor' (aka 'unsigned long') to 'mapped_type' (aka 'int') [-Wshorten-64-to-32] 111 | return G_map[id] = add_vertex(VertexProperties(id), G); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:118:31: warning: implicit conversion loses integer precision: 'typename config::vertex_descriptor' (aka 'unsigned long') to 'mapped_type' (aka 'int') [-Wshorten-64-to-32] 118 | return G_pruned_map[id] = add_vertex(VertexProperties(id), G_pruned); | ~ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:413:10: warning: variable 'total1' set but not used [-Wunused-but-set-variable] 413 | double total1=0; | ^ PCSF.cpp:221:29: warning: implicit conversion loses integer precision: 'value_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 221 | current=*second; pred=p[current]; | ~^~~~~~~~~~ PCSF.cpp:224:89: warning: implicit conversion loses integer precision: 'value_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 224 | while(pred!=current){perPath[outer][inner].push_back(current); current=pred; pred=p[current]; } perPath[outer][inner].push_back(current); | ~^~~~~~~~~~ PCSF.cpp:518:7: warning: variable 'uncovered_nodes' set but not used [-Wunused-but-set-variable] 518 | int uncovered_nodes = 0; | ^ PCSF.cpp:445:16: warning: implicit conversion loses integer precision: 'reference' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 445 | root = *ei; | ~ ^~~ PCSF.cpp:457:12: warning: implicit conversion loses integer precision: 'value_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32] 457 | father=spanning_tree_G_pruned[ancestor]; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:464:14: warning: implicit conversion loses integer precision: 'value_type' (aka 'unsigned long') to 'unsigned int' [-Wshorten-64-to-32] 464 | temp=spanning_tree_G_pruned[father]; | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:482:31: warning: implicit conversion loses integer precision: 'value_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 482 | predecessor[i].father=spanning_tree_G_pruned[i]; | ~^~~~~~~~~~~~~~~~~~~~~~~~~ PCSF.cpp:490:49: warning: implicit conversion loses integer precision: 'size_type' (aka 'unsigned long') to 'int' [-Wshorten-64-to-32] 490 | predecessor[i].size=predecessor[i].children.size(); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 29 warnings generated. clang++ -mmacos-version-min=26 -std=gnu++20 -I"/Users/ripley/R/R-devel/include" -DNDEBUG -I'/Users/ripley/R/Library/Rcpp/include' -I'/Users/ripley/R/Library/BH/include' -isystem /opt/R/arm64/include -fPIC -g -O2 -Wall -pedantic -Wconversion -Wno-sign-conversion -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:79: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/sugar.h:33: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/functions.h:63: /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:38:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 38 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:44:20: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 44 | s += t/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:68:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 68 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:69:15: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 69 | si /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:77:20: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 77 | s += t/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:78:22: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 78 | si += ti/n; | ~^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:104:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 104 | s /= n; // no overflow correction needed for logical vectors | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:122:14: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 122 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/sugar/functions/mean.h:128:16: warning: implicit conversion from 'R_xlen_t' (aka 'long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 128 | s += t/n; | ~^ In file included from RcppExports.cpp:4: In file included from /Users/ripley/R/Library/Rcpp/include/Rcpp.h:93: /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:399:14: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 399 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:407:22: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 407 | s += t / n; | ~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:426:14: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 426 | s /= n; | ~~ ^ /Users/ripley/R/Library/Rcpp/include/Rcpp/algorithm.h:435:22: warning: implicit conversion from 'std::size_t' (aka 'unsigned long') to 'long double' may lose precision [-Wimplicit-int-float-conversion] 435 | s += t / n; | ~ ^ 13 warnings generated. clang++ -mmacos-version-min=26 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Users/ripley/R/R-devel/lib -L/opt/R/arm64/lib -o XYomics.so PCSF.o RcppExports.o -L/Users/ripley/R/R-devel/lib -lR installing to /Users/ripley/R/packages/tests-devel/XYomics.Rcheck/00LOCK-XYomics/00new/XYomics/libs ** 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 ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (XYomics)