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### Running command:
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### rm -rf BiocNeighbors.buildbin-libdir && mkdir BiocNeighbors.buildbin-libdir && F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL --build --library=BiocNeighbors.buildbin-libdir BiocNeighbors_2.0.1.tar.gz
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* installing *source* package 'BiocNeighbors' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
using C++17
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c annoy.cpp -o annoy.o
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:10,
from annoy.cpp:15:
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1188:30: required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1410:24: required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Euclidean; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:969:46: required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:265:23: required from 'knncolle_annoy::AnnoyPrebuilt<Distance_, Dim_, Index_, Float_, InternalIndex_, InternalData_>::AnnoyPrebuilt(const Matrix_&, const knncolle_annoy::AnnoyOptions&) [with Matrix_ = knncolle::L2NormalizedMatrix<knncolle::SimpleMatrix<int, int, double> >; Distance_ = Annoy::Euclidean; Dim_ = int; Index_ = int; Float_ = double; InternalIndex_ = int; InternalData_ = float]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:359:16: required from 'knncolle::Prebuilt<typename Matrix_::dimension_type, typename Matrix_::index_type, Float_>* knncolle_annoy::AnnoyBuilder<Distance_, Matrix_, Float_, InternalIndex_, InternalData_>::build_raw(const Matrix_&) const [with Distance_ = Annoy::Euclidean; Matrix_ = knncolle::L2NormalizedMatrix<knncolle::SimpleMatrix<int, int, double> >; Float_ = double; InternalIndex_ = int; InternalData_ = float; typename Matrix_::dimension_type = int; typename Matrix_::index_type = int]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:358:97: required from here
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1309 | children_indices[0].size(), children_indices[1].size());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:64: note: format string is defined here
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ~~^
| |
| long int
| %lld
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1309 | children_indices[0].size(), children_indices[1].size());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:88: note: format string is defined here
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ~~^
| |
| long int
| %lld
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h: In instantiation of 'S Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::_make_tree(const std::vector<T>&, bool, Random&, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Manhattan; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1188:30: required from 'void Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::thread_build(int, int, ThreadedBuildPolicy&) [with S = int; T = float; Distance = Annoy::Manhattan; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1410:24: required from 'static void Annoy::AnnoyIndexSingleThreadedBuildPolicy::build(Annoy::AnnoyIndex<S, T, D, Random, Annoy::AnnoyIndexSingleThreadedBuildPolicy>*, int, int) [with S = int; T = float; D = Annoy::Manhattan; Random = Annoy::Kiss64Random]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:969:46: required from 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::build(int, int, char**) [with S = int; T = float; Distance = Annoy::Manhattan; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:265:23: required from 'knncolle_annoy::AnnoyPrebuilt<Distance_, Dim_, Index_, Float_, InternalIndex_, InternalData_>::AnnoyPrebuilt(const Matrix_&, const knncolle_annoy::AnnoyOptions&) [with Matrix_ = knncolle::SimpleMatrix<int, int, double>; Distance_ = Annoy::Manhattan; Dim_ = int; Index_ = int; Float_ = double; InternalIndex_ = int; InternalData_ = float]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:359:16: required from 'knncolle::Prebuilt<typename Matrix_::dimension_type, typename Matrix_::index_type, Float_>* knncolle_annoy::AnnoyBuilder<Distance_, Matrix_, Float_, InternalIndex_, InternalData_>::build_raw(const Matrix_&) const [with Distance_ = Annoy::Manhattan; Matrix_ = knncolle::SimpleMatrix<int, int, double>; Float_ = double; InternalIndex_ = int; InternalData_ = float; typename Matrix_::dimension_type = int; typename Matrix_::index_type = int]'
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/knncolle_annoy/knncolle_annoy.hpp:358:97: required from here
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1309 | children_indices[0].size(), children_indices[1].size());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:64: note: format string is defined here
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ~~^
| |
| long int
| %lld
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:29: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1309 | children_indices[0].size(), children_indices[1].size());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1308:88: note: format string is defined here
1308 | annoylib_showUpdate("\tNo hyperplane found (left has %ld children, right has %ld children)\n",
| ~~^
| |
| long int
| %lld
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Manhattan; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1069:8: required from here
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1118 | if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1118:48: note: format string is defined here
1118 | if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
| ~~^
| |
| long unsigned int
| %llu
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h: In instantiation of 'bool Annoy::AnnoyIndex<S, T, Distance, Random, ThreadedBuildPolicy>::load(const char*, bool, char**) [with S = int; T = float; Distance = Annoy::Euclidean; Random = Annoy::Kiss64Random; ThreadedBuildPolicy = Annoy::AnnoyIndexSingleThreadedBuildPolicy]':
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1069:8: required from here
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1118:39: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
1118 | if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~
| |
| std::vector<int>::size_type {aka long long unsigned int}
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:81:66: note: in definition of macro 'annoylib_showUpdate'
81 | #define annoylib_showUpdate(...) { __ERROR_PRINTER_OVERRIDE__( __VA_ARGS__ ); }
| ^~~~~~~~~~~
F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include/annoy/annoylib.h:1118:48: note: format string is defined here
1118 | if (_verbose) annoylib_showUpdate("found %lu roots with degree %d\n", _roots.size(), m);
| ~~^
| |
| long unsigned int
| %llu
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exhaustive.cpp -o exhaustive.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c find_mutual_nns.cpp -o find_mutual_nns.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c generics.cpp -o generics.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c hnsw.cpp -o hnsw.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c kmknn.cpp -o kmknn.o
g++ -std=gnu++17 -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I../inst/include -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/assorthead/include' -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c vptree.cpp -o vptree.o
g++ -shared -s -static-libgcc -o BiocNeighbors.dll tmp.def RcppExports.o annoy.o exhaustive.o find_mutual_nns.o generics.o hnsw.o kmknn.o vptree.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/meat/BiocNeighbors.buildbin-libdir/00LOCK-BiocNeighbors/00new/BiocNeighbors/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'BiocNeighbors' as BiocNeighbors_2.0.1.zip
* DONE (BiocNeighbors)
