############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf dreamlet.buildbin-libdir && mkdir dreamlet.buildbin-libdir && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL --build --library=dreamlet.buildbin-libdir dreamlet_1.5.0.tar.gz ### ############################################################################## ############################################################################## * installing *source* package 'dreamlet' ... ** this is package 'dreamlet' version '1.5.0' ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 14.2.0' using C++11 g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include' -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c colsum_beachmat.cpp -o colsum_beachmat.o In file included from E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:11, from E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/beachmat.h:24, from colsum_beachmat.cpp:1: E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:95:27: warning: 'virtual const double* beachmat::lin_matrix::get_row(size_t, double*, size_t, size_t)' was hidden [-Woverloaded-virtual=] 95 | virtual const double* get_row(size_t r, double* work, size_t first, size_t last) = 0; | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:338:38: note: by 'beachmat::lin_sparse_matrix::get_row' 338 | sparse_index get_row(size_t r, double* work_x, int* work_i) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:66:24: warning: 'virtual const int* beachmat::lin_matrix::get_row(size_t, int*, size_t, size_t)' was hidden [-Woverloaded-virtual=] 66 | virtual const int* get_row(size_t r, int* work, size_t first, size_t last) = 0; | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:338:38: note: by 'beachmat::lin_sparse_matrix::get_row' 338 | sparse_index get_row(size_t r, double* work_x, int* work_i) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:81:27: warning: 'virtual const double* beachmat::lin_matrix::get_col(size_t, double*, size_t, size_t)' was hidden [-Woverloaded-virtual=] 81 | virtual const double* get_col(size_t c, double* work, size_t first, size_t last) = 0; | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:321:38: note: by 'beachmat::lin_sparse_matrix::get_col' 321 | sparse_index get_col(size_t c, double* work_x, int* work_i) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:52:24: warning: 'virtual const int* beachmat::lin_matrix::get_col(size_t, int*, size_t, size_t)' was hidden [-Woverloaded-virtual=] 52 | virtual const int* get_col(size_t c, int* work, size_t first, size_t last) = 0; | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:321:38: note: by 'beachmat::lin_sparse_matrix::get_col' 321 | sparse_index get_col(size_t c, double* work_x, int* work_i) { | ^~~~~~~ In file included from E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:12: E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 36 | return std::unique_ptr(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 38 | return std::unique_ptr(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::SparseArraySeed_reader::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from 'beachmat::lin_SparseArraySeed::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl]' 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from 'std::unique_ptr beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl]' 40 | return std::unique_ptr(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: 'const size_t' {aka 'const long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: 'int' and 'const size_t' {aka 'const long long unsigned int'} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long long unsigned int; size_t = long long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]' 596 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of 'beachmat::sparse_index beachmat::Csparse_core::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long long unsigned int; size_t = long long unsigned int]': E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from 'beachmat::sparse_index beachmat::SparseArraySeed_reader::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]' 650 | return core.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from 'beachmat::sparse_index beachmat::lin_SparseArraySeed::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long long unsigned int]' 602 | return reader.template get_row(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ E:/biocbuild/bbs-3.21-bioc/R/library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: 'const int' and 'const long long unsigned int' [-Wsign-compare] 250 | if (idex != *pIt && static_cast(i[idex]) == r) { | ~~~~~^~~~~~~ g++ -shared -s -static-libgcc -o dreamlet.dll tmp.def RcppExports.o colsum_beachmat.o -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR installing to E:/biocbuild/bbs-3.21-bioc/meat/dreamlet.buildbin-libdir/00LOCK-dreamlet/00new/dreamlet/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 'dreamlet' as dreamlet_1.5.0.zip * DONE (dreamlet)