############################################################################## ############################################################################## ### ### Running command: ### ### chmod a+r SIMLR -R && F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data SIMLR ### ############################################################################## ############################################################################## * checking for file 'SIMLR/DESCRIPTION' ... OK * preparing 'SIMLR': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package 'SIMLR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 12.2.0' using C++ compiler: 'G__~1.EXE (GCC) 12.2.0' g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c Rtsne.cpp -o Rtsne.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c package_init.c -o package_init.o gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c projsplx_R.c -o projsplx_R.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sptree.cpp -o sptree.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c tsne.cpp -o tsne.o tsne.cpp: In member function 'void TSNE::computeSquaredEuclideanDistance(double*, int, int, double*)': tsne.cpp:883:11: error: too few arguments to function 'void dgemm_(const char*, const char*, const int*, const int*, const int*, const double*, const double*, const int*, const double*, const int*, const double*, double*, const int*, size_t, size_t)' 883 | dgemm_("T", "N", &N, &N, &D, &a1, X, &D, X, &D, &a2, DD, &N); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from F:/biocbuild/bbs-3.17-bioc/R/include/R.h:78, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp/r/headers.h:66, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/RcppCommon.h:30, from F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include/Rcpp.h:27, from tsne.cpp:39: F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:10: note: declared here 207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m, | ^~~~~ F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/RS.h:77:25: note: in definition of macro 'F77_CALL' 77 | # define F77_CALL(x) x ## _ | ^ F:/biocbuild/bbs-3.17-bioc/R/include/R_ext/BLAS.h:207:1: note: in expansion of macro 'F77_NAME' 207 | F77_NAME(dgemm)(const char *transa, const char *transb, const int *m, | ^~~~~~~~ tsne.cpp: In member function 'bool TSNE::load_data(double**, int*, int*, int*, double*, double*, int*)': tsne.cpp:967:48: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 967 | if (fread(*data, sizeof(double), *n * *d, h) != *n * *d) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from tsne.cpp:41: vptree.h: In instantiation of 'void VpTree::search(Node*, const T&, int, std::priority_queue&) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance; typename std::vector >::value_type = VpTree::HeapItem]': vptree.h:131:15: required from 'void VpTree::search(const T&, int, std::vector*, std::vector*) [with T = DataPoint; double (* distance)(const T&, const T&) = precomputed_distance]' tsne.cpp:472:21: required from here vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue::HeapItem, std::vector::HeapItem, std::allocator::HeapItem> >, std::less::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results) | ~~~~~~~~~~~~^~~~ vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue::HeapItem, std::vector::HeapItem, std::allocator::HeapItem> >, std::less::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list) | ~~~~~~~~~~~~^~~~ vptree.h: In instantiation of 'void VpTree::search(Node*, const T&, int, std::priority_queue&) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance; typename std::vector >::value_type = VpTree::HeapItem]': vptree.h:131:15: required from 'void VpTree::search(const T&, int, std::vector*, std::vector*) [with T = DataPoint; double (* distance)(const T&, const T&) = euclidean_distance]' tsne.cpp:550:21: required from here vptree.h:237:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue::HeapItem, std::vector::HeapItem, std::allocator::HeapItem> >, std::less::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 237 | if(heap.size() == k) heap.pop(); // remove furthest node from result list (if we already have k results) | ~~~~~~~~~~~~^~~~ vptree.h:239:28: warning: comparison of integer expressions of different signedness: 'std::priority_queue::HeapItem, std::vector::HeapItem, std::allocator::HeapItem> >, std::less::HeapItem> >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare] 239 | if(heap.size() == k) _tau = heap.top().dist; // update value of tau (farthest point in result list) | ~~~~~~~~~~~~^~~~ make: *** [F:/biocbuild/bbs-3.17-bioc/R/etc/x64/Makeconf:264: tsne.o] Error 1 ERROR: compilation failed for package 'SIMLR' * removing 'F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/RtmpaavDRb/Rinst3e7c6a6424a4/SIMLR' ----------------------------------- ERROR: package installation failed